Just found this out today. What I mean is, for example at the end of act 6 you enter the boss with 90 ninpo and usually throw away until you have 50 and then kill the boss. If you instead had ended the stage with the extra 40 ninpo, you would transition into act 7 at the exact same time. There is just a window of dead time that gets filled to countdown extra ninpo if you have any.

This is NOT true in ninja gaiden I, where you lose 3 frames per ninpo. I'm pretty sure it's irrelevant in ng3, since you use your ninpo on all of the bosses (and the countdown is so fast anyways).

BTW Scumtron knew about this in 2007 when he made his TAS, but no one paid any attention to it...