Flagg's Madness Manipulation through Crimson King's eyes should be troublesome, even for the Bounty Hunter. That's probably the only part of Flagg's Mind/Madness kit which can work on the Bounty Hu-- Nvm. They are restricted.
Flagg's Commands could have been troublesome (Not that it is completely useless here) if the Bounty Hunter hasn't resisted the effects of the whole Herald event + Djinn Magic, which are like the highest level of Madness/Mind hax for that tier without some form of connection to a higher entity.
Bounty Hunter still possesses his passive Probability, Curse and Death Manipulation + BFR.
Bounty Hunter also has the Wandbreaker which nullifies magic. He also has the AP advantage, his meteors should be more powerful than several Lightning Bolts.
They both can control Souls and Death. With Bounty Hunter being at an advantage due to Life Manipulation.
Illusions shouldn't be a problem as the Bounty Hunter can resist them, although he needs some focus.
Overall, the Bounty Hunter should take this, due to his classic Passive Hax, and a tiny AP advantage.
I want to ask this right away, just on general principle.
If the Bounty Hunter can resist mindhax and null magic, what exactly can Flagg do to him? Barring prep and some miscellaneous equipment (neither of which he has access to in this fight, for good reason), that's effectively his entire arsenal right there.