I have the Elmar 50/3.5 and had the R3A, and they were a good combo, particularly b/c you can shoot in AE mode and forget the fiddly aperture lever on the lens.
To answer your question: The 50/3.5 Elmar will not collapse completely into the R3A (I don't believe it will collapse completely in any Bessa body). However, there is a workaround. Here's what I do w/ the Elmar on my Bessa T, and did w/ the Elmar on the R3A: get an elastic hair doodle (the kind used for tying hair in a ponytail) and wrap it several times around the lens barrel. It acts like a bumper. The lens can be partially collapsed, but not so far that it will collide w/ the inside of the camera. A rubber band can also work.