The class quests were originally meant to be something you did at the "correct" level, so they actually lined up nicely enough. I played MNK for SB's launch, and I did the quest in parallel with the MSQ so they weren't out of place, but yeah if you do them separately or after the fact, they don't make much sense but I think it's part of the suspension of belief you have to accept when playing a game. It's like if you go and do Coil for the first time after finishing the current MSQ, just won't make sense but they can't really be like "ah too late you missed the time to do this story, you had to do it right after 2.0". And it's good world building too to include the corresponding classes with the events of the game that matter for them.