A very intresting point! While this is, of course, very true, I'm afraid i don't think that it'll be very relevant to transferring from planet to planet. The whole thing is relative to the body you're currently in orbit (or not) around, and so when moving from one body to another, the velocity readout changes. In a mission to another planet, the most efficient way to do so is (at least as I see it) to move to orbiting Kerbol and then grow the orbit out to the other planet. But I digress. The system should work perfectly fine for interplanetary transport, just as it does for Mun-Minmus missions. Besides, the only time I really use it is when I'm coming down to a body, and I don't want to know my total velocity relative to Kerbol at that point.