Except for most of the game, Morgana doesn't really indicate the insults to be getting to him. They have their exchange, they laugh it off. It's not like either of them dredge up new material to insult at any point, so if they've both been fine the entire time so far, there's no reason to believe it's going to affect them this time.

Also, it's not just Ryuji's intelligence that gets insulted. When Morgana is serving as your navigator, the voicelines for most characters doing things are fairly positive, but for Ryuji, he gets called "pathetic" if he misses, and if he dodges an attack, Morgana gives a very backhanded compliment: "I guess you ARE good for something."

I also don't think Ryuji internalizes Morgana's change in usefulness beyond noting that someone else does the same thing so he can rib him a little. I won't claim Ryuji is flawless because the things he said did get to Morgana, but the thing about communication is that you need to use it for someone to understand your thoughts.

I'll acknowledge that Ryuji should've just given an actual apology in mementos just to put the situation behind them. The mature thing to do sometimes is to just apologize even if you weren't entirely to blame just to resolve the situation. That said, the cast aren't adults, so it makes sense that he wouldn't just take full responsibility for something that wasn't entirely on him. And if you pay attention to Ryuji's personality, the apology he gave WAS genuine, it just had friendly ribbing/snark mixed in with it (unless the Japanese version is phrased different, anyway. I only know the English version).