This is an interesting thread, but there's a part of this problem that no one has addressed. The relative points of impact of bullets at different velocities depend entirely on where in their trajectories you look.
Although the slower bullet will be launched at a steeper angle than the faster bullet, it will also be falling faster at any given distance than the faster bullet. Thus, the slower bullet will have a more arched trajectory than the faster bullet. At some point the two trajectories will cross and the points of impact will be the same. At any point closer than that, the slower bullet will strike the target above the faster bullet, but beyond that point the reverse will be true. So the answer to the question is really "It depends where you look.".
This phenomenon will be true of both rifles and handguns and has nothing to do with the ratio of bullet to gun mass.
Also, if you clamped a gun in vise to eliminate the effects of recoil on trajectory, the bullets would not hit in the same place; the slower bullet would always be below the faster moving one due to gravity.
