Even if FATE tried its best to resist any change, I doubt that it would be possible for everything to be exactly the same. Maybe some fish was swimming in El Nido waters, noticed a strange landform that wasn't there the day before, so it decided to swim towards Zenan instead, so some fisherman got one more fish for dinner one night. With an extra fish the fisherman decides that he has enough fish that he can take the day off the next day, and builds a hut during the day. Then a storm comes later that year and one person that normally didn't get shelter survived in the fisherman's hut. Now, one person's life/death can obviously make huge differences (as apparent in CC).
It's possible that FATE could predict what fish originally came to El Nido and didn't swim to Zenan so that it could capture them and what fish originally came to El Nido and back to Zenan so that it could let them go free, but even then it would be highly unlikely that it could actually control the entire ocean surrounding El Nido to make it act as if there weren't an island, or that capturing fish that didn't go to Zenan originally wouldn't have an effect on other fish and consequently have a much larger effect.
If the game said anything about Dino/Chronopolis' existance not effecting the Chrono world until 900 or w/e, then I'd make the assumption that FATE could control the weather surrounding it and control the fish to make them swim as they normally would, but the game makes no such claim as far as I know. It's similar to the Belthasar thing; if the game never said that Belthasar planed out CC, no one would believe the faint possibilities that he did so.
Moreover, even if there weren't a different up until Porre colonized, Porre's military power would have an impact on Crono and co. If Crono and co. act differently, then they'll affect the past differently, so even after 65,000,000BC there'd be some difference.
