I just came across this old forum post, the one with the “secret” tags for footnotes and annotations. This seems to work for all kinds of imported documents in Scrivener. Is it safe to use? Any possible pitfalls? I’ve prepared an experimental version of my Mellel2MMD converter that treats footnotes in this manner and so far it seems to work.
You should be safe to use them, as they are unlikely to change any time soon. If those tags occur in an imported document, the imported document gets converted to RTFD and placed inside the project file wrapper and then when it gets opened inside Scrivener those tags should be successfully converted to footnotes/annotations. I think using them in the sort of converter you are talking about would be a pretty good use of them. Just make sure that there is always a matching end tag, obviously (not that it would break Scrivener, but it would mess up the footnote/annotation ranges).
All the best,