Maybe I'm misunderstanding you but - bah? Different models and renders are not handled like this at all. Fighters each have their own folder containing model and motion data for slots 1-8 (or c00 to c07).
There's a parameter file that controls how many alt options a fighter has (the engine has support for more, up to 255 per fighter) as well as what entry in the fighter name file any given slot will use (Used for Olimar, Bowser Jr. and Steve but can work with anyone). Meanwhile the renders are handled in the same way, with the same parameter file dictating how many a fighter has and in turn, which ones to load on the CSS.
Bowser Jr., a character with eight full-fledged character swap alts, takes up one slot, the same as Captain Falcon who's got nothing but basic recolors. Sephiroth's shirtless alt is not taking up another fighter slot. No fighter is taking up more than one, unless for whatever reason you counted echoes.