That would be a more interesting and imaginative twist, but that just makes it all the less likely that these writers will go that way. No, I think they're being very literal about the whole thing.
It does lend credence to Arthur Petrelli's claim that Sylar never needed to open anyone's skulls to gain powers. Maybe the only reason he ever latched onto that habit is because of a messed-up need to imitate Dad? Otherwise, it's one hell of a coincidence.
It's never made a whole lot of sense to me that he needs to actually look at someone's brain to gain powers - what is he seeing? Does he have microscopic vision? Why doesn't he have the same type of vision towards other things?
But what does make sense: he gains powers via proximity and doesn't realize it. When he starts trying to gain powers, he convinces himself that he needs to imitate his two Dads to be effective - the skull cutting of bio-dad, and the observation skills of watchmaker dad. Those were never necessary - just an outgrowth of his mangled psyche.
If these writers want to start trying to stitch together all the dangling threads of Sylar's characterization, they could start by establishing that he never actually needed to kill anyone, and his mimickry powers really do happen through proximity or "empathy" or something. And the rest is due to his messed up personality. Plus his powers really do drive him to kill on top of it all. Gah, he's still a mess.
Of course they use the aforementioned method.