I think Riddel's supposed to tell you to go to the El Nido triangle if you go and talk to her after Terra Tower opens up, though idk if that's contingent on having done the Dario or Marbule sidequests or whatever. There's other in-game stuff directing you to get Starky, it's just earlier than you really need him -- around the time you're doing the dragon quests iirc. Also I don't remember why but I DID get the impression that there was a translation issue there making things more confusing than they were supposed to be.
Though yeah that's like the one part of the game that annoyed me (besides hrr drr late Square PSX game hrr drr two megs of ram hrr drr getting like 10 frames per second here), although that's more because Starky's kind of a dingus and you don't really get his backstory until you get one of the New Game+ endings for some reason.
I don't think there's anything else particularly wonky after that -- maybe the correct way to beat the last boss, but that's supposed to be taken as more of a Myst-styled observational puzzle.