Yeah, pretty much got that covered. I've been designing and implementing software for close to 40 years, and and using "evolving" documentation applications for that long as well: Word, TeX/LaTex, Format (ancient IBM mainframe), Script (updated Format), Bookmaster (updated again), some old Bell Labs tag language I can't even remember, SAS documentation language, SGML, HTML, XHTML, CSS, FrameMaker, and probably others I've forgotten. Both the eBook and the PDF submitted to KDP are solid (and not complex) -- with only this one warning that I actually anticipated.
I'm not even certain that the cloud reader won't support what I've done -- since these things are sensitive not just to which features you've used, but how you've used them. If someone had said "No, don't worry about it. That warning is left over from older implementations and doesn't apply any longer," I would just leave things as they are. But I think at this point it's just not worth taking the chance when a half-hour or less of work can remove any risk.
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