Doublecross: According to TFwiki he is two minds in one, I don't have him so I've never considered it.
Flywheels if I had him and Animated Bliztwing when I get him are each one character. Multiple/split personalities are mental illness, not separate minds in real life AFAIK.
Never saw BM so I'm not familiar with Beast Changer.
Punch/Counterpunch is an Autobot with a Deception alt mode, in the cartoon at least, don't know about Marvel comics.
I'm not sure about the Quintesson's, I'd have to research it if they ever release a toy thats not Alpha Q which I hate and will never pick up.
G1 Metroplex, I see I have them listed as one, but I'll have to research them now that I see that I have them listed that way (oversight maybe). All I know is only Metroplex was shown to have a consciousness in the show, I don't know about the comics. Generations Metroplex I'd say Scamper is is own guy in this version.
Optimus, again in the cartoon, sorry I never read the Marvel comics, Roller is only ever seen as a drone and in IDW all three are one consciousness as explained in the first few issues when Megatron almost kills Prime.
This is why I keep a separate number that is just complete sets, as counting by character is up to interpretation.