Bottoming out is completely normal. The point is to not bottom out hard.
^^This. If you're still accelerating the key when it hits bottom the shock is strong. If you're already reducing the force (or have even changed its direction) it's not so strong and in fact can help "rebound" the finger if you're actually already putting in upward force to overcome the momentum.
F=ma, v=u+at, s=ut+1/2 at^2, p=mv
so position and force are 2 derivations apart. Which means you can still bottom out even while applying upward force already. This is why I always install trampolines on my switches.
In order to not bottom out, you need to apply some very precise amounts of force at very accurate timing to allow the slider to move past the actuation point, but not reach the bottom out point. Very hard to do (especially at speed as the forces required are greater and the timing more precise) and ultimately not all that valuable. As long as you're not bottoming out strongly, you're doing okay.
[EDIT] I don't really want to, but I can do some calculations to support this if needed. [/EDIT]