Thanks for weighing in!
Just to be clear, I'm not necessarily expecting things to stay magically compatible – I only am looking for a way to remove overlaps, but leave any points intact that are on the exterior of that combined shape. I think you understood my meaning already, but my initial image was pretty ambiguous, so this shows my general hope better:
So, it sounds like the way the Remove Overlap functionality works, it's not that these points are removed as an extra step, but rather that their removal is a core part of the function? And there's no way to "turn that off"?
As a simple temporary solution, I have found that I can at least have a visual of missing points by duplicating the glyph to an "overlap" layer, then turning that layer's visibility on.
You could run a pre-overlap code getting points that are going to be removed... and add them back in a post-overlap script
Is there some kind of accessible list of points to be removed (that doesn't seem very likely), or would I have to find a way to loop through points, and mathematically determine if they're on a straight path?