Well, I have answered my own question, Film magazines are indeed cross-compatible between Contarex & Contaflex. I don't know what the pin mentioned is for, and some backs do NOT have it in place for sure. But I have the Contaflex Super BC and one of these (just dug it up) and it does have the pin. Looks like it may be controlling frame counter on the Contarex (does not appear to do anything on Contaflex but there is a recess below advance lever that accepts that protrusion. At least on Super BC with magazine on, frame counter on top advances along with one on magazines bottom.
So my question is answered, just now am wondering what this pin is for.