Too overwhelmed to say more than what you said, but I would note that the VE doesn't actually change. I do know why you said that however, and I'm just playing semantics IMO. Tristan could probably explain why better than I, as I recall it was his prof that brought it up.
The main reason turbo cars get better mileage MOST of the time is simply due to the fact that there is far less pumping loss. Even when the engine is operating in relative vacuum, there is still generally less vacuum at part throttle than with an NA engine simply because (as Bryan said) the compressor is always pumping some air. "Boost" doesn't have to bring the manifold pressure to positive to have an effect, although people usually use the term only in that context.
@shot: It doesn't make much of a difference for the same reasons as above, at least in a reasonable application like a street car where the turbo can get into it's efficiency range without ludicrous amounts of throttle and rpm.
