It's always the same game : you spend hours trying to figure out a problem, then a few seconds after having asked for help you figure it out.
It works now, I was probably just missing the slash before the question mark in the URL (so rewrite rules indeed, I guess).
Thanks. I understood from your post and a bit of search that ProcessWire was using TinyMCE by default, and found out I could switch to raw textarea through "setup > fields > body > details" in the admin panel — which is for the better, since I'm not fond of rich text editor and prefer writing HTML.
Indeed the stripping is done by TinyCME, so not using it obviously enables rendering of MathML without further action.
Adding MathML valid elements as suggested in your edit should also work (didn't test), but I guess people willing to use a rich text editor would prefer to use one of the plugins you linked to — though most are quite old, not sure they still work ?
Thanks again !