I thought I'd set up some flavor, but you can go to the second paragraph for the crux of the question
Just to set up some context, I'm going through my second playthrough as a Rauataian mercenary (Bleak Walker/Assassin) hunting down a god mostly because I'm being forced to and partly because getting the rest of my soul back would probably be pretty nice. So, I decide to I gather up some companions to make things easier and it just so happens to that I run into our familiar friend Pallegina again. I'm thinking we have work history together and she keeps things professional, so I figure why not and I bring her along. A nice exploration of the Deadfire while an adra colossus rampages in the background later, it is time to choose a faction to help get me to Ukaizo. While I'm no Maia, I thought I might as well pick the home country since I'm being presented the choice. Of course, Pallegina doesn't like this and leaves, and considering I practically finished the entirety of the game with her, I respect her decision and we exchange farewells with her even saying that we might even see each other again. How nice!
Fast forward to Ukaizo, there stood the VTC ships ready to intercept us, I thought nothing of it and blew right past them. Fast forward again, and there they are on the island for the final showdown and to my surprise, alongside them was none other than Pallegina ready to face off. Although, there was a slight sting, my character was ready to remorsefully cut down anyone that got in his way (which I ultimately ended up doing) but I decided I would rather avoid that scenario altogether since it pained me to end a companion OOC. My understanding was the enemy faction that shows up is the one you have the worst relationship with, so I reset to before choosing a faction, and I pissed of the Principi until my reputation with them was worse than with the VTC. However, going through the process of choosing my faction and getting to Ukaizo again, the VTC were still the ones to be there, so I guess I'm confused as how the enemy faction in Ukaizo actually works.