I would say, apples and oranges. Its actually easier to make the jump that Tigh and friends are Cylons then to some how make it work that a Known Cylon with many sisters is also the "Final Five" Cylon. I can accept the Final Five are different in nature some how. Not so easy to work out the logic of Sharon/Boomer's model is somehow not akin to her fellows.
Indeed. Note the way that argument's proponents have framed it:
The Boomer and Athena models are physically identical but otherwise subtlely different. Three recognized Boomer as the Final Cylon.
Okay, that argument is self-defeating. Three only has the faces of the Final Five to go by. If Boomer and Athena are physically the same, then Three wouldn't know the difference.
It's much easier to believe that the face she saw was either a face we've not seen or the face of somebody like Socrata Thrace, who, when she died downloaded into a different body altogether. So Three saw the face of Socrata, but now Socrata lives in a different body, so the Final Cylon is still somebody in the Fleet. She just doesn't know it.