Would increasing the difficulty from Officer to Agito increase the amount of EXP earned from battles while doing secret training?
No, but you can speed things up by going in to the secret training, then after you are sent to the main menu - go to the XMB (or whatever the PS4 equivalent is now called) and change the date to a day in advance. Save changes and load your save, you now get a ridiculous high amount of XP for that character, you can literally max them out in minutes.
Be careful as this reduces the challenge of the game considerably and even at level 40 you can pretty much beat anything in the main story without any tactics or thought.
(changing the date backwards after your boosting has no effect on the game or XP)