I mean, it's not just the quantity of games but FE was pretty established by the time it was added. Andy has different problems such as being less prominent in JP.
Sakurai's logic for Rex is fine for base roster, but for DLC, idk. Maybe they made plans pretty early, but Xeno2 has been out for a while now. Given that Joker was presumably nowhere near complete when he was revealed and that the rest of the characters are likely not very far into development, I don't see why they couldn't have course-corrected for Rex if they wanted. If he misses the boat for DLC, as it seems to be the case, it's no longer a fault in timing. Rex is an established character now. Only thing he no longer has is the same degree of relevancy, and if that is what puts him out of the running then it's a fault in the character selection process rather than "oh he had bad timing." If the game's been out for as long as it has, who cares anymore? The character is available for use, and we know how well his game did critically and sales-wise, so opting not to use him is a conscious decision.
Keep in mind that this doesn't have to do with my personal views on Rex. I'm not especially attached to him, but while timing may have messed up his base roster chances I don't think that's the right scapegoat if he misses out on DLC.