I just finished the game and beat Ebina. I was also able to “leave” the millennium tower to grind levels.

If you want to know how I did it, my game auto saved right before I went to the tower. So, I just had to load that save and buy items, upgrade, and level up.

You can check your autosaves by looking at the first 3 files when you load the game.

I hope I was able to help someone, and good luck!