Yep, whenever you start the petition for a Free Company is where your company allies (I started the petition in Limsa and tried to turn it in in Ul'dah and they wouldn't let me).
Same, except it was the Maelstrom for me. My best guess is that since people weren't affiliated with a Grand Company, the only faction that could rise was the one that the Free Company was allied with.
If we're going to try to centralize Free Company information in this thread, maybe it should be moved to Advanced Theorycrafting? Not really sure how much theory there will be and how much will be explicitly stated, but knowing Squacks...