It is really rather pointless in giving level settings when our systems and rooms are are so very different. My amp sits out in the IB enclosure so it's a bit of nuisance going in an out just to change settings.
But if it makes you happy:
I tend to leave my EP2500 controls at 3 o'clock.
I use the controls on my active crossover (sitting within easy reach in the rack) to raise and lower the bass levels relative to the speakers. The settings depend on whether I'm watching films or listening to music. I raise and lower the bass by anything up to an indicated 8dB according to the media and my mood. I am no longer a perfectionist when it comes to calibration. Though I will quickly change the settings if something sounds subjectively bass heavy or light. This very rarely happens. I hold the opinion that the better the sub the less sensitive one is to excessive bass. It may simply be that my room is kind to all bass levels. All bass just sounds incredibly clean and completely boom-free. I put this down to the lack of parallel walls, sloping ceilings, multiple levels and low dwarf/knee walls.
BTW: I have never seen the fourth bar on the BFD nor have I ever seen the EP2500 clipping lights come on.
I can't really answer your last question. Obviously large dynamics will cause clipping. I'm not sure of the frequency relationship. Presumably it would be BFD filter dependant.