"Peak voltage" is nimh terminology, for lipo, its max voltage. There really is no peak - lipo would go right on charging til there was a problem.

Since I don't have a Passport, I can't be sure, but there has to be some kind of termination order - charger should always terminate on max 4.2v/cell voltage - period. Regardless of what capacity is, if voltage reaches 4.2v/cell, lipo charging stops. The only time charger should terminate on capacity is if the "cut off capacity" is reached before the voltage reaches max of 4.2v/cell. This is the reason for the 'headroom'.

So if you charge a 3/4 charged 5000mah lipo with the capacity set at 5500, if the max cell voltage is ignored for this discussion, yes, the charger will then terminate on capacity when it reaches 5500mah. Realistically though, if cells are correctly rated, I'd expect termination when max cell voltage is reached. Its only if the cells are underrated that you'll likely terminate on capacity if you have it set to label capacity. If it bothers you, set it on the label capacity and see where it terminates.

If its 5000mah, you know it will hold more - the closer the cells are to 4.2v/cell, the less the additional mah will amount too. If the voltage is low, then there will be more to potentially add for capacity until voltge reaches cell max voltage.

If the cutoff is approached gradually, 3v is fine. The reason its set higher while running is there are big voltage swings due to big amp demands from the motor due to tigger finger 'requests' - setting lvc higher while running protects the lipos from these big demands and there resulting voltage dips. Charger discharging is much different - the demand is steady and not subject to the big swings like seen onboard.