nobody thought to say the obvious??
people don't typically have any problem standing up their snatches, though (myself excepted).
well dear, thats because you need to do your back squats!!
seriously, though... i have trouble with finding a pain free high bar placement. i have traps - but i can't seem to find a sweet spot where it doesn't feel like it is crushing the vertebrae in a bad way. i have started doing low bar back squats where i can find a pain free if not totally comfortable place for it. hopefully i can move the bar up as i progress.
i do think it is important to get the body (joints, ligaments etc) used to the heavier loads.
i also think it is important (for me anyway, even if not oly lifting more generally) to really get the squat to be a smooth and automatic movement. with the loads in different places etc. i'm not sure that there will be negative motor interference from different squat patterns... it is about the body doing what is most efficient (hence natural) given different task demands... but maybe not... i have crazy theories sometimes (my last one was that one only needed to front squat for oly lifting)