I suspect the status immunity may be tied to the class, actually. It is certainly not a feature of FE8 bosses in general to be status immune, so Lyon is special there.
Anyway, 3 goes through the ruins qualifies as clearly aftergame to me, so definitely voting on the boss form regardless. It's at least as much him (more, really) as is the case for bosses like Jecht, Dhoulmagus/Leopold, Saki, etc.