Installation of a shorter stem
As long as you're putting on the same size stem (steer tube size, not length), which you should be doing unless it came with spacers/shims, then yeah no problem.

If the clamping area is taller, you may need to get a longer bolt to reach the star nut, but then you'll also have some stem above the steer tube and that's no good either. Odds are though that you'll be just fine switching over.