I am having the same problem. Had the trans rebuilt (bearings, syncros, springs, etc, no gears). On the way home I noticed the same restriction of the boot. I had replaced the original shifter with the GMM-Street version and the boot then remained loose. I took it back to the transmission shop - put it on the rack and checked what we could. There is not really much that could be "put on wrong". Still a dilemma to me.
05 M6, peddarized, GMM Ripshift Street, Magnaflows, H-pipe, JBS shorties, Swede OTRCAI, one piece driveshaft, dash gauges, skip shift delete