No, membranes don't automatically bottom out. However, it seems that way because in order to actuate the switch mechanism, you have to bottom out.
With Topre switches, you don't have to bottom out entirely. The capacitive switch under the rubber actuates about half way down. So if you learn to type really softly, you can touch type on a Topre board without ever bottoming out.
I tend to bottom out most of the time because I have large hands. If you have that kind of problem where you tend to bottom out, I'd suggest the 55g board. It's got the best all around balance of stiffness and smoothness.
For me, 45g is borderline too soft.