Oh, hi Ken! I guess I didn't look at the header at all before replying to your post; I just dug straight into your sample files.
Authors do weird things all the time.
They do, don't they? <long-suffering sigh>
The symptoms you describe (like "TNR for text but Calibri for section signs") sound exactly like what I get when I'm doing a project for some state DOJ or other. I am not sure how they are getting their section signs, but it seems clear that they're not beying keyed per se; perhaps they're from the Insert Symbol menu, and they're getting marked by one of the default Calibri-based Word character styles? But that is neither here nor there; you'd need a post-import cleanup method that won't remove all the other local formatting and style overrides that you need to keep, and it sounds like you already have that.
The tweak I'd suggest is that you add "searching for text marked as Arabic" to your text-cleanup strategy. Or perhaps a Javascript like "find anything in this document that isn't marked as English: USA and flag it for review" might be best. I don't often have to deal with dozens of Word-file submissions anymore, but when I do, I usually use a script that I made years ago, modified from Jongware's PrepText. There are a few similar scripts floating around out there, but if you're dealing with many "creative" ways of typesetting a subscript, maybe Kasyan's version might be worth looking at?
I can't really change the client's workflow, except maybe to point out to them that someone somewhere is getting these section signs in via an Arabic keyboard.
Well, our clients aren't going to change their workflows for us, right? Especially when the issue is that someone, somewhere once opened a Word doc that had complex scripts used somewhere in it. I once struggled against some persistent Word-cruft for years before I discovered that someone in the local county health department had decided that the Latin-script glyphs from the Windows default Thai UI font were much prettier than Arial or Calibri, and so she used it as her font for all documentation, and therefore 100% of the Word files from her were filled with spurious complex script information.