A puzzling fenomenon indeed!
First, I use an M2 (1958), M3 (1965) and an M6TTL (2002), all of which have a consistent frame spacing of about 2,5 mm. The space allways falls exactly between two sprocket holes.
I really wonder if the bag or case has anything to do with the erratic spacing that you have experienced. The advance lever should advance the film exactly 8 sprocket holes, not more. On the M4 through M7 the rewind knob is indeed active at all times (as opposed to the M2 and M3), but turning it in the advance direction will only unwind the film in the cassette, untill it jams against the inside. I don't believe this will actually move the film across the gate. Turning it in the opposite (rewind) direction will pull the film firmly against the spool, but you need to exercise considerable force to retract any film without putting the rewind lever on "R". You are most likely to strip the sprocket holes this way.
I can only think of two possibilities: (1) the film advance mechanism needs to be inspected or adjusted, or (2) the shutter curtains need to be adjusted. Possibly the film gate is never completely exposed, even at speeds under 1/60, because the first curtain has become lazy and doesn't travel all the way across the gate before it is caught by the second curtain. Are your negatives exactly 36 mm wide? What you are looking at may not be uneven spacing but a small (about 2 mm) edge of the negative remaining unexposed because of a shutter issue.