You only need to reverse the phase on one of the pickups, not the other, so that they're out of phase with each other when combined. So, you will only need one push/pull for the phase switching, and one push/pull each to split the pickups (which leaves you with potentially one spare push/pull).
You could use the extra push/pull to allow you to link the two pickups together in series when combined (rather than the standard parallel) or use it for tone capacitor switching etc. And yes, you still have the extra hole to use for a kill switch, either a small toggle (On/Off or On/Off/Momentary) or a momentary push button.