I may be wrong, but I'm getting the sense that something happened to Starbuck that has made her a hybrid. She's still the same Starbuck, and she didn't begin life as a Cylon, but on the journey to and from Earth (whichever Earth that maybe - one or even both), something (or someone) did something to her so that she's now a human-Cylon hybrid.
Why? Because back in Faith, watch carefully...
When Emily died, Roslin saw here in her dream/vision.
When the Six who attacked Jean died, Natalie was with her.
When the Eight was killed, she turned to Athena, but Athena rejected her, so Anders stepped in and took her place.
When the Hybrid was deactivated and "died," Starbuck was there with it. Indeed, that same hybrid was deactivated and a few episodes later came back online.
Note the pattern:
Emily each one was with a person of like "kind." Emily was with Roslin, a human with the same disease. Natalie, a Six, executed the other Six. If Athena had not rejected Eight, two Eights would have been together, but upon rejection, Anders stepped in, so the Eight was with another Cylon. What's left? Starbuck and the Hybrid. IMO, that's a message...Starbuck has been hybridized. She's not a constructed hybrid. She's not a born hybrid like Hera. She's either had her DNA changed or she died after all and there are other Cylons (like on Earth, eg. "Earth 2") who resurrected her and in so doing replicated her which stands very much in parallel to what happened to the hybrid, it "died" and then "came back." It even came back with a mission, just like Starbuck "died" and "came back" in Maelstrom and 4.01. Perhaps what Starbuck was wondering about herself in 4.01 wasn't so far from the truth after all. Consider also, she returned in a brand new Viper, an exact replica of the one in which she "died." IMO, there are Cylons on Earth 2 and they are capable of replicating humans perfectly, even downloading their consciousnesses into those replicas (which would anticipate the Cylon Project in Caprica by extension...what happened before, eg. on Earth, happened again..on the Colonies) - but not multiple replicas of the same person, rather one replica per person at any given time. Earth is the place, metaphorically speaking, where humanity can achieve eternal life if they so choose, but they have to prove themselves worthy of it - which is why, IMO, the Earth 2 Cylons are interfering so that the humanity and their Cylons have to work together.
Indeed, that sounds precisely like something Dualla (yeah, I know, I still say she's the Final Cylon) said in Season 2...children are separated from their parents. Rifts need to be healed, families need to be brought together. IMO, that's the Final Cylon's mission, but somewhere along the way it may have gotten it's own ideas ahead of the mission, which could be why things have gotten so fouled up or it may have royally screwed up the mission early on. Either way, it's probably been in communication of some sort between Earth 2 and wherever it's located the whole time.
It's probably just one Cylon on a mission, completely separate from the other Four, yet aware of them. It's mission is different than theirs. Instead of learning about humanity, it's mission is to bring humanity and Cylons together.
Maybe it found the Cylons as I said before and thought it would try helping them by helping them evolve to become more like mankind, thinking that if it could make them less like machines, humanity would be more accepting and the Cylons would be more understanding, leading to peace, reunion, and eventually full reunion with the 13th tribe itself. But the Cylons from the Colonies decided to commit patricide instead. So, it blames itself for bringing abt. the destruction of the Colonies, which would explain why the Prime Hybrid in Razor said it was seeking redemption.
IMO, it knows where Earth 2 is, but it's not going to tell anybody until it fulfills some sort of prime directive, namely it can't bring anybody from either group to the final destination until humans and Cylons have resolved their differences, or at least one side has done all it can to make peace but has failed every last possible attempt and the other side won't reconcile, probably because the Cylons on Earth 2, after the holocaust of Earth 1, won't have it any other way. Think about it, their first home was completely destroyed, do you think they'd allow it to happen again? They've learned their lesson, so they aren't about to let humans and Cylons in their current state arrive there and bring their war there. IMO, either neither group is allowed to arrive at Earth2 in conflict with the other, or (B) the side that has tried to reconcile but failed is allowed to arrive and will receive the help of Earth 2 when it does.