Near the area where you fight the Overgrown Treewalker, you can enter one of the caves to find a secret hideout. There's a dead wizard here, and you can read some of his research notes. They all talk about a kind of magic called nullomancy, and it's never outright said, but everything written here matches up with how ????? behaves throughout the game! The notes are unfinished though, so we still don't know everything about what a nullomancer like ????? might be capable of.
There's an extra appearance of ????? you can see during the festival at the end of the game if you have 100% completion. If you go into the forest area at the edge of the festival, there's a scene where ????? puts an item on the ground and leaves before your characters walk in. The item is a little trophy to congratulate the team on their accomplishments!
When you visit the castle concert hall, most of the time there's a singer up on the stage. But if you come there right before the final journey into the Spire, nobody is there, and you can have Moka go up on stage and sing! This doesn't change anything else in the game, but it's a pretty nice scene.
The spell Erase Memory usually just stops an enemy from using one of their moves, but it can secretly be used to end the Betrayed Guard fight early. If you use this move on the first turn of the fight, you'll erase the guard's memory of why he was fighting you in the first place! You only unlock this spell at a pretty high level though, so you'll need to make sure you're giving enough XP to the right character.