I'm not here for arguing against linguistic concepts, so let me cover just one thing:

> None of this helps to explain why there might be a conflict between Markdown and agglutination, though.

reST, not Markdown. (Yeah I totally get it though because I made the same mistake in the OP!) Those languages often need to highlight individual morphemes inside space-separated "words", but reST assumes space-separated "word" as a default, hence annoyance.