There's only so much you can shorten it before you run out of threads on the bolt, so plan your cut with that in mind. Shorter bolts can be found if you need more shortening, but you can't add threads with a cutting die because the existing threads are rolled not cut. So the shaft diameter is too small to have threads cut into it.

Another issue that could bite you in the future is that the stem will still have a minimum insertion line, but it won't be correct anymore. Someone in the future, you or the next owner, may mistakenly raise the stem to an unsafe height , believing the line and words stamped in the quill.

I have shortened a few stems but never came up with an easy solution for that. Maybe stamp a new mini-insert line, and hope the future person sees it and stops there.