FWIW, I think I'd take into account how much of a penalty there is by the "end" of the joining floor.
If catching up is trivial - say, a Suikoden series character who for whatever reason joins underlevel and unequipped, but a trip to the blacksmith and 5 battles changes that - no penalty, pretend they joined up immediately. If a character takes some effort to catch up, but not an inordinate amount? A small penalty until it'd be overcome in game. By the end of Moonbase, Peppita / Sophia are probably still a bit underlevel and you had to take time to carefully not let them die at lvl. 1, so I'd give them a small stat penalty until Floor 5 or so. If a character is very hard to catch up and the slow start penalty is noticable until the very end, like say Nino? I'd probably start with a big penalty but tail it off to a small penalty and no penalty as if the character joined earlier than they did. So Nino would suck floors 1-2, and still have a small penalty floors 3-5, say.
The trickier case might be when a character does in fact need to be 'caught up', but the catching up is in DL-illegal skills... say VP2 Silmeria being bad because she doesn't have everyone else's cool (illegal) toys or, to a lesser extent, characters like Meliadoul / Orlandu needing to play 'catch up' on their job tree. No idea there, aside from maybe a small stat 'disrespect' penalty.