I think Baker's rhythms show through. Of course, we're talking about a very low bandwidth channel of information, relative to the amount of information that an actor puts out under normal conditions.
I don't think it really matters anyway to the amount of credit that Baker deserved. If the character of R2 (yes, he's a character) is of the sort that performers who can play him perfectly are interchangeable, then Baker was such a perfect performer, and Baker's performance constituted the prototype.