Ahhh, it's the iPad3! (not jailbreak related) The minimum brightness on my iPad3 is very low and as far as I can tell, identical to the lowest system brightness setting versus lowest iBooks setting.
Looking at my iPad1, which I have to hand, there is a difference as you describe. The brightness is still linked, but iBooks definitely has the ability to go a little lower! When you switch back to the home screen the brightness pops up just a little..., then back down when you switch back to iBooks.
Because of the awesome screen, I've used my iPad3 almost exclusively for all reading tasks since I got it. Guess I've become too used to it!
Thanks, I've learned something today! But at least there is a link between system and iBooks brightness levels "up to a point"