My verdict would be that the Pocket Dimension is unnecessary and thus should be discarded.
Most of what is to follow has been stated before, but these are my reasonings for such a conclusion.
Regarding Phenomena G, that Lavos survives defeat and goes into the DBT, wouldn't it be the other way around?
Let us say that Crono & co defeat Lavos in 12,000 BC. The Lavos that they had encountered in 600AD with Magus is no longer there: time has been changed and that Lavos is discarded to the DBT, along with the rest of the timeline. That Lavos is then the one that merges with Schala, while in the real world there's a Lavos corpse rotting somewhere. If Lavos is still aware, then it is aware that it is outside of time and could deduce that it has been defeated "in the past."
Regarding Phenomena F, that Lavos' shell is present in the Ocean Palace Incident even if you defeated it previously, that seems to be specifically an attempt to break the game. Generally, it requires a New Game + to do, correct? Just as the endings that are generally only accessible through NG+ are of dubious canonicity, it would seem actions that are generally only possible through NG+ are likewise so.
Regarding Phenomena D, that Lavos imitates the Guardian Robot which is "in the future" from all perspectives except the battle in 1999 AD, reason demands that we must conclude that Lavos is drawing from the memories of Crono & Co. If Lavos is instead drawing directly from history, then we have the curiosity that Lavos happens to choose only those creatures that Crono & Co fought, and only at the times in which they fought them. Between 65,000,000 and 2300 there have never been any better creatures for Lavos to emulate than those that Crono & Co just happened to face.
Regarding Phenomena B, specifically that Lavos is at the same power regardless of era in which one fights him, too much importance may be placed on that. Generally, once creatures reach adulthood, their strength and size does not increase dramatically. A black bear at the age of 7 will be about as fearsome as a black bear at the age of 10. While there will be changes, those are comparatively small when put next to the changes between child and adult. Lavos has been feeding on the planet since 65,000,000 BC and "growing stronger," but it is entirely possible that all such energies when into reproduction and assimilation, not towards increasing its raw strength. Furthermore, the earliest we can fight Lavos is 12,000 BC. That gives him 64,988,000 years to develop and grow strong, whatever that means. In contrast, the 13,999 year difference between the earliest and the latest one can face Lavos seems negligible.
Which only leaves us with Phenomena A, 1/2 of B, C, and E.
Regarding A, I actually have a question: assuming this is the blue aura while fighting the outer shell, does the aura not appear in any time period? For example, if one takes the bucket (or the telepod gate in NG+) to 1999 and fights Lavos, does the aura still appear?
If the aura does not appear when fighting Lavos in one Time Period, then I think we could reasonably say that the aura is a gate effect transporting the team to the time period in which the aura is not present (and the period in which it isn't present, it is missing because it is unneeded). This would seemingly specifically counter the PD theory, as the aura should always be present.
If, however, the aura is present in all time periods, then I believe it would be reasonable to suppose it is a random battle effect with no meaning or that it is a Pocket Dimension.
I think I recall that there is a way to battle Lavos without this aura, but I have no save game with which to check, nor am I in a location where I can check.
Regarding Phenomena C, like with the bosses I think we must conclude that the focus is on Crono & Co's experience. Again, Lavos does not warp to any period but only those to which the party has been to. While one might say that Lavos also warps to points of significance in its own life or the life of the planet, the fact that Leene Square is included seems to refute that. It is important to Crono and Marle, but I see no reason that it is important to Lavos or the Planet.
Regarding Phenomena E, this would seem to support the supposition that Lavos is defeated in 1999 AD and facing him at any other period brings one here.
Regarding Phenomena B, the first half, it would likewise seem to support the conclusion that one faces Lavos in 1999.
As an aside, if TB is ever debunked, then Lavos would have to be defeated in 1999 (or 1000) so as to not change the course of 600 AD.