REPORTING BACK: I found the problem. I had checked “Make Overhangs Printable,” and this is what caused the problem. When doing so it actually does warn you that it might change the model’s geometry, but I had forgotten that warning. Frankly, I don’t actually remember setting it in the first place, so maybe it was just a haphazard mistake I made in the past without realizing what it did and that followed me around up until now. Well, thanks to this breakdown, now I know what it does and what the trade-offs are.