Hmmm, now that I've seen the Caprica trailer...perhaps the way to reconcile Leoben's comments and D'anna's comments is something like this.
The 4 have been to Earth. Presumably they are from Earth.
The Seven are the generation of Cylons that are the result of the First War.
The Final Cylon is the First Cylon.
So, there aren't 2 types or generations of Cylons. There are 3:
1 from Earth.
1 from the Colonies, all machine.
1 from the Colonies, machine modeled on human, a human personality d/loaded / copied as a replica of an actual human. It's actually a hybrid of human and machine.
The First Cylon from the Colonies is Joe Adama's daughter, and Bill's sister. It would make sense of Leoben's comment. It would mean the face D'anna saw was her face, and face not among the fleet. It's also the Fifth Cylon of the "Final Five" group because of its characterisitics
, but not because of its origin
However, it could still be in the fleet, for it has simply transferred its own consciousness into a different body, a body similar to the original, yet different enough that it's well hidden from Cylon and human alike. This could fit something Virtual Six said to Baltar in the mini: "Really, we should make a copy of your brain pattern..." The Graystone prototype seems to be the result of that. So, if it just periodically downloaded that same pattern into a different body, not a copy of the original one, in order to hide itself, it could still survive, looking physically different, while in a virtual environment, it might look just like the original, eg. Joe's daughter.
If so, then I'm still of the opinion that's its Dualla, because of what she said about leaving her father and losing faith in God back in her interview with D'anna in Season 2. She told the truth. That could well be what happens to the replica of Adama's daughter in Caprica. It adopts monotheism, comes to believe in God, an ancient belief secretly passed down since the time of Kobol, and eventually it leaves Adama after some sort of conflict, and later it loses its faith in God. Later, the Cylons devolve into mechanical models, which in turn evolve back into humans later on. Its struggle for redemption may be because its somehow at the center of all of this. The end of humanity on the colonies began with it. Heck, if the destruction of Earth's society is relatively recent, we now know it doesn't take that long to reach Earth from the Colonies, so its possible after whatever happens in Caprica it went to Earth and somehow the dark cloud that seems to follow it, so to speak, went with it, eventually resulting in the war on Earth. It may have escaped and taken the Four with it as survivors. Heck it may mean the Four thought they were human because they were downloaded into replicas of themselves and never suspected it, unlike the Seven who knew they were Cylon because they were made by Cylons.
However, she clearly is strongly fond of Bill, not just Lee, which is something you might expect if she had the "soul" of his sister.
Objection 1: Cavil said he was "Number 1." Yes, but there's a discrepancy in the numbers. It skips over 7 and goes to 8. Perhaps Cavil is covering up the truth, the numbers are really 2 to 8 and 9 to 12, with 1 being the prototype. The reason Cavil seems to have assigned it, implicitly, the number 7 is that Graystone was right, it's a "perfect" Cylon. In Gematria, seven is the number of perfection.
Objection 2: Eww, then Lee married his aunt. Yes and no. Can a copy be considered an "aunt?" Maybe marrying Lee was her way of becoming an Adama again.
Objection 3: What about the Virtuals? Well, they could be the same being. If so, perhaps what we've been seeing as the virtuals is from Earth. It's a "13th" Cylon, the fifth one of the group from Earth. The Final Cylon could still know all it knows on this theory if it's been in contact with the Four, been to Earth itself, or in contact with the Virtual/s at any point. In short, it stands between the Four and the Seven. It stands with the Five, because these 5 are all "perfect" Cylons, apart from the others. Yet, because it's not from Earth, it doesn't hear the music the others hear.
This theory could also accommodate the idea that Boomer or Athena is the one of the "Final Five," for, if we redo the numbers, making the replica Graystone creates Number 1 and Cavil to Caprica Six, 2 - 7, then the Eights would be part of the Final Five, the only ones with multiple copies for some reason, while the other 4 have none.