If you have the room on the other side, just reverse the bolt. Easy and free.
Yes, that is your alternator - it looks like a CS-series. Let me guess - 1987-1990 rig?
As far as that "huge shoulder" you mention, that's a standard. Capscrews are threaded for a length equal to three times the nominal diameter - for, say, a 3/8" screw, that's 9/8", or just over an inch. If the screw length is less than that, then the screw is fully threaded.
Note that screws are usually plated to prevent corrosion - if you're going to cut the screw (nothing wrong with that, I do it quite often,) replace it with stainless or paint over the end to seal it. Note that primer is porous - it's not meant to prevent rust, just to make the paint stick better.