The only thing that matters is main quest level. Being overleveled is unhelpful, unless you get to a really high level like 50 or 60 and buy really high item level crafted gear so you can destroy open world mobs. But since your chocobo helps you to survive those open world mobs there's no reason to worry about it.

The main reason you would overlevel is from doing daily roulettes or having an experience bonus, such as the one you get for being on a Preferred world which doubles quest experience. The experience gain from main quests for 1-50 used to not be enough and only got you to 47-49, but it was adjusted recently so that could be why.

Additional levels don't matter very much, just item level, so you don't need to worry about it.