About Porre overthrowing Guardia and FATE letting Porre make such a change:
As a couple people said, the 1000AD in CC isn't the same 1000AD as in CT. Also, everything from 65,000,000BC and onwards is a bit different than it was before the time crash, since the time crash influences Crono and co. and they influence 65,000,000 and other time periods.
Also, if FATE decided to just capture the Porre people that came to explore and not let them leave, that would probably have just as much of an effect as letting them gain power through elements. Imagine half of Porre suddenly disappearing without explanation. The only way that FATE could possibly limit changes would be for it to have brainwashed all the settlers that came and made them think that they found empty ocean, but I doubt that they wandered into Chronopolis (was the sea of eden closed off at that time) or that FATE could send brainwashing things to meet them without even bigger changes.
I don't think the game actually says anything specifically about Lynx's killing Serge, so I've always just took it to mean that Wazuki was just going crazy and killed whatever was closest to him (maybe he was playing with Serge on the beach, went crazy, and just killed him) or he specifically targeted Serge because he loved him the most. This, however, wasn't a coincidence and Belthasar probably 'planned' for Wazuki to be the one to become Lynx because that would cause the dimensions to split. Also, maybe FATE was aware that doing this would cause the dimensions to split, and wanted two frozen flames or something.
Also, does the game say that FATE's goal is to ensure its being built in the future? Unless I missed something, its only goal was to ensure that Lavos gets defeated, and even trying to make itself built in the future would be a stupid thing to plan for since it's not like Chronopolis would just evaporate because it was 'never' built.
Finally, onto Kid's pendant. I actually think that the pendant is a major plothole. How exactly does rewinding time help? If it worked like the dagger of time (Prince of Persia: the Sands of Time), then it would make sense; Kid would see herself about to get killed, rewind time, and, knowing the future, prevent it. However, it doesn't, apparently. If it only rewinds time after Kid dies, and she has no recollection of it, how does rewinding time actually change time to ensure her survival? It just seems to me that Kid would get killed, rewind time, get killed again, rewind time, etc. If I'm missing something, please fill me in.