Personality System Data Collection [WiP]

Okay, no idea if it's been answered but here goes.

Currently, all traits are at the 500 exp. per day cap. However, looking at the John's Last Present quest, it gives 600 exp.

Would you gain all 600 EXP. or just 500 of it and the other 100 would be wasted?

You would gain it all.
In fact, I think you would gain all 600 even if you were at 499 before you did the quest.
At least, that's how it works with Ambition: I regularly get my ambition to 495+ (1 Zak, 2 Pap, and a few random area bosses) and then do zak or von leon, and end up with around 800 Ambition for the day. (It says 500/500 in the window, but looking at the actual Ambition value, I know I received the full amount).