Wow! I see it now... same two layers being merged produces different results between Merge Down and Merge Visible. This is crazy.
Again, it should just work... It's atrocious that you want to give 'guidance' to someone who expects something to work the way it should, and instead of seeking to have it sorted out, you're looking to find out what the user is doing wrong. This kind of thinking won't help anyone.
Second, why not try a sample file that's created, and that clearly demonstrates the issue at hand? Stop being so defensive and acknowledge that there is a problem.
I repeated the same process in Adobe Photoshop, and there was no discrepancy between Merge Down and Merge Visible.
BTW, I'm on Windows 10, so this is not a Mac OS bug. It is common to both.