Version A keeps the vanilla experience penalty (which subtracts 3 base exp. per character level), so that eventually enemies will stop giving experience on kill (like in the base game, bats with an experience value of 8 stop giving experience at level 3, as the "subtraction" is 9 and equal to or more than what it gives, which is clamped to 0 exp). Like the base game it would still motivate going on higher NG+ runs to counteract it.

Version B removes the experience cut per level found in the vanilla game, so that bats will always give 8 experience (as seen in the Bestiary) - thus disregarding the experience penalty in its entirety.

I should've been more clear about it so I added a small description update.

TL;DR - Version B disables the experience penalty in vanilla HoH entirely (so you can keep earning experience regardless of where you are in the game), while Version A keeps the penalty to stay in line with vanilla progression.

Sorry but what is the difference between Version A and B?