Plus you're ignoring a massive fact, which is that the pendent did do it. This is exactly what we see at the beginning of the game. It's actually a canon fact. Whereas the "the entity did it" theories lack any basis on this level.
What "it" are you referring to? The pendant, presumably due to its abilities to manage energy, did activate the time distortion that sent Marle into the past, as well as Chrono a few minutes later. But that isn't the "it" that "the pendant did it" or "the entity did it" are referring to. You are claiming that it is because of the pendant that Marle can be subject to the grandfather paradox.
Let us take a specific look at your suppositions:
1) Marle could have been subject to a "time crash," in a similar manner that Chronopolis seems to have been subject to such a crash.
2) Chrono, though he was subject to a very similar set of circumstances, experienced a different sort of time travel since he held the pendant (Marle having dropped it).
3) Marle, lacking the pendant, is subject to the grandfather paradox.
4) Chrono, with the pendant, has full TTI.
The problem with this is that the technology behind the time crash and Marle' disappearance are inherently different. It would be paramount to saying that adding the pendant to a horse could turn it into a space shuttle! The timecrash utilized the frozen flame, which is notably absent from Marle's disappearance. Even those problem aside, the time crash "expos[ed] the entire Sea of Eden outside the time stream;" the time crash alone didn't send Chronopolis back it time, rather it seems to have moved it outside of time (thus, sort of like the End of Time). Lavos, sensing it and realizing that it would be defeated, then brought it back to the past in an effort to change the future enough to change its own fate.
Even assuming Marle experienced a time crash, that would have just put her outside of time; it would have taken a Lavos-like being to actually transport her to 600 AD. The only two beings like that that we are aware of are Lavos and the Entity.
As Crono 99 pointed out, the time crash created a black dome in CC; Marle, however, went through a standard blue portal. Thus, even the physical appearance of the two circumstances appears to not be the same.
Problems with the Marle/Time Crash portion of your theory aside, your theory necessitates that when exposed to the same set of circumstances, the pendant provides TTI if one holds it through the entirety of the process. As you put it, you are proposing that the pendant protects against TTI-less time crashes. Why should this be the case? There is no hint of this anywhere else in the game. As for the gatekey, you are assuming that Lucca was able to duplicate this ability based on just what she saw and was able to deduce? She is smart, but that is like saying that if she saw a nuclear explosion she could easily figure out how it was done! Furthermore, the pendant is made from dreamstone, the gatekey is not. The pendant needed the telepod reaction to cause the gate to open, the key can open it on its own. These two objects are different in almost every regard.
Your theory works, but it is quite convoluted. Given that the only time your theory can even come into play is when an individual starts a time crash with a pendant like device but doesn't carry that device back in time with them, I would say your theory has almost no practical value for determining future events. As such, it is really just a patchwork explanation, not a theory.
Just a random,
Thought