I like your theory! I don't know if we can definitively say that the time travel HAS to take us to the same place tho--like with the timesplicer stones at least, we know that those link between both different times AND spaces, and so the same could be said for surfer dude's manipulations. At this point it's just hard to say.
I still agree that Zone Zero is/was Hiyoshi City tho, I mean it was the last known place Indriad was operating, and I feel like the END dungeon (where you fight Gardevoir) could easily be where the destruction begins, due to not only Indriad, but possibly all of the Garufan magic the three protectors were bound to be using. Nymiera even said before they headed out that this would be their final mission, and the text was gold to boot. Plus all the E, N, and D unowns makes it less than subtle that something definitely came to an end here.