I suspect the gravitational slingshot is an artifact of the domain of influence approximation that they're making and the timing of the crossing of the boundary. If you approach a planet retrograde to its orbital motion rather than direct, you should lose rather than gain momentum relative to the system. I haven't tried to see if this is the case for the Kerbol system. I think a simple 2-body algorithm should conserve the energy of the each interacting body although their momentum vectors will change although the sum will remain unchanged. So long since I thought about this stuff that I'm probably talking bollocks.
BTW if a Kerbie touches a monolith, does Also Sprach Zarathustra ring out and the little guy get a bit brainier? I suppose the Mun and Kerbol have to be in the right alignment. That's another thing - I wounder if there are eclipses.