About this scale bar thing, I think you tuned in to the second part of a two-part discussion. The first part is HERE. It talks about your suggestion, which is dead on target if you're using a camera and a workflow that allows to set the magnification and have it stay set. Stanley's setup doesn't really allow that, so he was looking around for alternatives.
Regarding the issue of perspective on stacking, some of what you want is contained in the thread HERE, in a discussion of stack-and-stitch and telecentric lenses. Note in particular the first column, bottom row, of the second image. There is some more basic theory that may be helpful in an article HERE. That article focuses on explaining the No-Parallax Point for stitched panoramas, but its relevance here is that it talks a lot about what apertures really do. Some of that is pretty counterintuitive, like the illustration that you can change the angle-of-view of a lens by sticking an aperture plate in front of it! There is also the FAQ: What's the best way to focus when stacking?. I can't think of any published discussions that deal specifically with alignment in focus stacking, but that might make an interesting addition to the FAQ.
My suggestion is to go read the references, think about the problem, identify what's unclear, formulate a question, and post that in the FAQ on focusing. I'll respond in detail there.
Best regards,
--Rik