The bigger bullet generates more force in the recoil moment that tends to push the muzzle up, then, as Scorch said, spends longer time in the barrel exerting that push. Taken together, both factors tend to cause the muzzle to have recoiled to a higher angle of departure at the moment the heavier bullet exits. There can be an exception in a barrel whose natural transverse vibration is on the rise when the light bullet exits and on the drop when the heavier on does. A gun whose loads are so timed can shoot the heavier bullet to the same or lower point of impact than the lighter bullet, but the lighter bullet load is likely to be less accurate as firing on the harmonic rise tends to cause vertical stringing.
The bullet drop you were counting on to cause the heavier, slower bullet to impact lower on the target is complicated by two things. One is that the speed difference alone simply doesn't count for much at 100 yards. From a critically damped machine rest mounted barrel (in other words, no barrel vibration contribution) a 150 fps velocity difference in two identical .308 bullets is only going to change point of impact on the order of a tenth of an inch at that distance. At 200 yards it grows to about half an inch, and at 300 to about an inch. That's why Audette Ladders are fired at those distances. You need some range to see a POI change due to velocity and barrel time differences.
The additional complication is that a heavier bullet of the same nose and base shape will have higher sectional density and ballistic coefficient. In other words, it bucks air resistance better. For that reason it can start out slower than its lighter brother, but at long range wind up actually going faster since it doesn't lose speed as quickly.
In the end, you want to develop a good sweet spot load for each bullet that the tables and good word of mouth say can do what you want. Learn how it behaves with your sights at different ranges (unless you intend it for just one target shooting range). For hunting, a good strategy is the late Jeff Cooper's recommendation to zero at 200 yards (about 2" high at 100 yards) for medium to large game. You then know that from point blank to about 240 yards, the trajectory won't significantly go above or below a 4" circle, and sight adjustments or holdover will thus be unnecessary unless you have a shot farther out than that.
