Well this is my first post, so excuse me if I am stepping out of line here or anything being a newcomer, but I've been reading this thread for some time now and thought I'd throw in a few of my own ideas.
Concerning the added ending: We see Magus inside the Dimensional Vortex, he says some meaningful Chrono stuff and then jumps in to save Schala. Well there is one thing I must ask...what happens if you kill Magus? Theoretically speaking, Frog killing Magus in the past should completely wipe him out if thats truly a future Magus, right? Yet no matter what, I bet you anything he's always there no matter if you kill his "past" self or not. So this brings up an interesting question in itself...
1. Is that really Magus?
2. Is he from another reality/universe?
3. Does this rewrite when the two worlds split?
4. Is it possible this is Magus from Radical Dreamers? And if so, does this mean it really is part of the canon and actually matters to the overall Chrono plot, or what?
Granted, my personal belief is it is a future Magus, but one cannot ignore these possibilities.
Concerning Magus being Guile: Its argued that Magus does not know how to exactly time travel, so he can't possibly be all that young as Guile appears in CC. Well I think everyone is forgetting one small piece of evidence here. The people of Zeal gained power from Lavos himself. Lavos is capable of effecting the space-time continuum aaaand...Queen Zeal herself can open gates to other time periods. Magus is her son, and unless this was removed from the new script, it is said Janus was more powerful than Schala, who appeared to be more powerful than Zeal (considering Zeal seemed to need Schala to do specific things, this conclusion seems to make sense).
Now granted, the age difference can be argued but I'll say this: If David Bowie can be sixty years old and look thirty-fourty, then a magical demon king who most likely can open up time-traveling portals can be fourty and look however the hell he wants imo (Though I'd like to see someone proove Magus' age, Toriyama isn't very good at realism). Guile could pass for thirty honestly. Now sure, Magus looks like a demon/fiend/mystic. But does anyone wonder if perhaps Magus' form in CT is a disguise? Remember, when he appeared to the Mystics as Janus, they attacked him. It would logically make sense to put on a disguise, use a Scythe, and appear more evil in order to frighten Guardia and keep the Mystics loyal to him. Really, why would magical power alter his physical form? Dalton clearly shows the ability to cast something similar to Dark Matter and he looks the same as ever. Also, Magus has used disguises in the past such as The Prophet. Now this was just a hood with shoulders, but either way he's used a disguise before to benefit himself. Whose to say Magus is nothing more than this? Its not even his real name, and Kato has had Magus go even further and go by Magil in RD.
Speaking of RD, I do believe one ending had Magil have amnesia and not know who he was, which sort of makes this make even more sense. Guile was...a bit too GOOD with Black elements, just happened to be able to float (not a common trait in 1020 AD), and his techs were too much like actual Shadow magic to be just coincidence. Sure, he was originally supposed to be Magus but he seemed too much like him to be altered to just be some dude who happened to be decent with magic. I'm not one for wishful thinking, but neither can I ignore the obvious.
Concerning the Dimensional Vortex: I am of the personal belief that this is either the Darkness Beyond Time, or similar to it. In which case, I do not believe that the Dream Devourer is something that happens after 1999, but something that occurred at the moment Lavos absorbed Schala. Now granted, I'm not exactly sure when the DD actually became what it is (it DOES exist outside of Time, so theoretically couldn't it exist at the same time as the normal Lavos?). Either way, I don't think it actually is at any particular point in time, as evidence to the Dimensional Distortion which seems to have various locations from multiple eras and locations throughout the game.
Either way, thats it for now. I think after I play the game I'll have more to say. So far from what I have see in videos and read, these are the conclusions I draw.