Yes, cutting back with the shoulder would mess with setting the finger pins properly. If you're using the minimal movement method of bumping, rather than cutting back the shoulder you need to offset the bump cuts towards the tip of the key.
It has the same practical effect of cutting back the shoulder without as much chance of messing with the finger pins. So when you tap the key, you are actually fully inserting the key and setting the finger pins with the side cuts on the key at the same time that you're bumping the lock and popping up the regular pins.
I haven't tried this yet, but at least theoretically this method should be able to bump Schlage Primus, ASSA Twin 6000, Scorpion CX-5 and similar sidebar locks (with separate sidebar pins) as long as you're using a blank with the proper sidebar cuts. I've been curious to experiment with it. I'd guess it won't be as easy as bumping regular pin tumbler locks and might take some trial-and-error to find the right amount of offset when moving the cuts towards the tip of the key, but it would be interesting to find out.