This way, there is not a countless amount of Lavos clones in the DBT, just one.
From our understanding, there wouldn't be a "countless amount of Lavos clones in the DBT" to begin with. Lavos exists in a pocket dimension, safe from any alterations to the timeline, because he doesn't fit in as a part of the timeline itself (in the way Crono and company do). You could remove the access to the pocket dimension, but that would not end Lavos' lifeline.
For example, you could travel back in time and divert Lavos' trajectory, but as he is in his pocket dimension, he gains TTI (through the same way Serge gets it, I was surmise, from dimension hopping), quite possibly to start draining the energy from the planet. So you can't do anything of that nature. However, this also goes to explaining why you have to go into the pocket dimension in order to defeat Lavos. Lavos could only be defeated in his dimension, where his timeline is a set path. Which is kind of smart on his part, when you think about it.
The Compendium holds that time travel events are protected by TTI. Therefore, Crono's appearance at Death Peak is assured, regardless of changes made to the past. The game, however, does not seem to share this view. We are told that we need an identical clone, which we then use to replace Crono. Why? Because the Grandfather Paradox does exist in Chrono Trigger. If the Entity cannot recall that Crono was killed, it will not recall the sequence of movements by the group made with intention to save Crono. The group will then be deleted and replaced by new counterparts, reflecting the future of Dreamline reacting to the new changes to 12000BC. Recall that this did not happen to Crono and Lucca when Marle vanished. This is because Crono and Lucca were at the Point of Change in 600AD that controlled events onwards, while the group described above was making a change to 12000BC that could have made incompatible changes to 2300AD.
The Compendium does not suggest, at least to my understanding, that time travel events themselves are protected by TTI. In the non-ruined future, you wouldn't see a ghastly image of Crono, Marle, and Lucca running through the sewers. It's a different timeline and those actions didn't take place in the non-ruined future. TTI basically ensures the memory of the events still exists. As long as Crono remembers watching the video of the Day of Lavos, he's able to stop Lavos. Although, it might be cool to have seen the non-ruined future and see Crono and company running around as ghastly images, only visible to those who can see through the timeline (i.e., Crono watching his "past" self learn of the Day of Lavos).
The Compendium has also suggested that the Grandfather Paradox does not exist, otherwise the entire game would be the biggest paradox ever heard of. Crono's appearance at Death Peak is not assured, as it requires, according to Gaspar, a certain amount of effort to be put into retrieving Crono for him to actually be retrieved. If it were an assured event, then all the rest of the group would have to do is just sit there and wait for him to show up. But this goes back to the Free Will theory, that inaction produces no action, and that until the group actually performs an action, the resulting chain of events does not yet occur. Until Marle and whoever the player picks to join her travel into the pocket dimension during that frozen second, and until they decide and will themselves to exchange Crono and the clone, Crono is not assured to appear at Death Peak.
Perhaps this lends credence to not necessarily a single event being the point of timeline alteration, but rather a checklist. Like, in order for Crono to appear once again, the following must occur: 1) The Time Egg is used at Death Peak; 2) A clone of Crono must be present; 3) The clone must be shifted into Crono's position and Crono be removed from where he was at; and 4) Crono must be removed from the pocket dimension. So it's a chain of events, and if all four of those do not take place, then the theoretical #5) Crono appears at Death Peak, cannot occur.
Marle Paradox
Leene is supposed to be saved at Time X, this is what the Entity recalls. Leene is, however, not saved at Time X - ultimately forcing her doom. We see, in game, that Yakra is moments away from killing Queen Leene in the Cathedral when we find them. It was, perhaps, not possible for Frog to save the Queen alone in time. Though Crono and Lucca intervene to make saving the Queen possible, this is only after the ultimate result has been witnessed: Marle ceases to exist.
When the three of them save Queen Leene, they create a new Time X within the Dreamline where Marle's family line is restored, therefore Marle's previous actions are recalled by the Entity, placing her exactly where she was first forgotten.
While I would initially reference my theory that a 50%-50% of something happening (50% of the time Leene is saved, 50% of the time she is killed, in this example) allows a timeline to stay in a sort of Limbo (which if you read my latest post on my discussion on whether the universe was split or duplicated in Chrono Cross, I state the theory could explain both Belthasar's statement that the 50-50 probability of Serge's life or death and the reasoning for the universe splitting and Another World not being shifted to the DBT due to the uncertainty), perhaps a modified version could be applied here. Notice how I stated that 50% of the time Leene is saved/killed, not Marle. Say whichever has the higher percentage of probability is what occurs. The moment one of the two options breaks 50%, it becomes the event in the current timeline.
Since Lucca arrived pretty much right after Marle "disappeared", we can safely assume that Lucca had gained TTI by this time. So, we have Crono and Lucca both with TTI. Let's say they decide to just sit around. Well, then Frog is left to go after Yakra by himself. Continuing on, let's assume that Frog makes his way through the cathedral until he reaches Yakra's room. Any idea of who is going to win in a Frog vs. Yakra match? Probably Yakra. Okay, so probability here is that while Frog's intervention delayed the Queen's death, it didn't prevent it. Then we can add in Crono and Lucca, and boom, the chances rise. For an example (and don't quote me on these being actual percentages, since we don't know), here's some example values to illustrate.
Remember, the Percentage theory (gotta think of a better name for it) states that until a choice rises about 50%, the timeline is in Limbo.
1. Timeline at start of game: Leene is kidnapped, but soldiers find her and defeat Yakra. Leene's survival rate: 100%. Leene survives and Marle exists.
2. Timeline after Marle time-travels: Leene is kidnapped. Marle has not yet chosen to interact with the citizens of the Kingdom of Guardia in 600, so the soldiers still find Leene and defeat Yakra. Leene's survival rate: 100%. Leene survives and Marle exists.
3. Timeline after Marle time-travels and Crono time-travels: Leene is kidnapped. Marle may not have chosen to interact with the citizens of the Kingdom of Guardia yet (this would allow for Lucca to travel back still), so the soldiers still find Leene and defeat Yakra. Leene's survival rate: 100%. Leene survives and Marle exists.
4. Timeline after all three have time traveled: Leene is kidnapped. While the soldiers are out looking for Marle in different groups, one small contingent finds Marle while the rest are looking in the Cathedral for Leene. When word is heard that "Leene" (Marle) is found, the search is called off moments before finding Yakra and the real queen. Crono is just now approaching the castle, and Lucca has appeared in the past, thereby giving her the TTI she needs to still be there.
At this point, we get to a slight discussion of how the Probability Theory (there, better name) takes effect. We have three possible outcomes at this point: a) Yakra kills the Queen; b) Yakra fights Frog and kills the Queen; c) Yakra fights Frog, Crono, and Lucca, and doesn't kill the Queen. At this point, until any action is made, there is a 66% chance (since until an action is made all probable outcomes have the same probability) that the Queen will die. So, the Queen dies since that probability is a 2 in 3 chance she'll die. However, becomes the timeline doesn't know which of the two timelines where she dies to utilize (where Yakra kills the Queen and then the one where Yakra fights Frog and then kills the Queen), the timeline is still in Limbo, which unfortunately has the side effect of removing Marle from the "timeline" (partially because she would no longer exist, but also because the timeline is in such a state of limbo that she's not shunted to the DBT).
5. The final timeline: Leene is kidnapped. While the soldiers are out looking for Marle in different groups, one small contingent finds Marle while the rest are looking in the Cathedral for Leene. When word is heard that "Leene" (Marle) is found, the search is called off moments before finding Yakra and the real queen. Crono watches as Marle is shunted into a state of Timeline Limbo due to the Probability Theory, and he and Lucca go off and help Frog defeat Yakra. Upon defeating Yakra, he can no longer kill Leene, and the one remaining timeline, where Leene is saved, takes precedence and the timeline realigns itself with the events of that outcome (which now has a 100% chance of happening). Leene's survival is now at 100% once more, and Leene is alive and Marle is returned from her Timeline Limbo state, as the probability she exists in this timeline is 100% again.