This might be a problem for third-parties who wanted to stand up something as evocative as "the Lua Foundation" without PUC-Rio involved. In some jurisdictions there's a duty for trademark holders to stop infringing uses (or else they lose the mark). So barring any agreement with PUC-Rio's lawyers, those lawyers may be obligated to sue a Lua Foundation, especially if were part of the name of a legal entity.
It might be helpful to post a trademark notice on the front page of
lua.org, if not the footers for the site.
I am not a lawyer. Consult local legal advice. If you want US help, post; a bunch of us may have contacts.