M:AFG was written before the Codex, so it couldn't take it into account (but "mortal poison" is something I think means "poison from the mortal plane (as opposed to the demonic plane), and it does not consider whether or not it is magical". The spells in the Codex, however, were not thinking about M:AFG when they were being written.
IMO, it is up to the individual GM to determine how it works in his setting.