It’s definitely the dynamic ride height that matters, not the nominal BB height or drop.
So with less travel you’ll have less actual sag (and often less % sag too) so the sagged height is higher for a given BB drop.
With a shock+leverage curve that has more mid-stroke support you’ll have a higher ride height in practice even if all else when statically sagged is the same.
With a suspension design that has more anti-squat you’ll have a higher ride height when pedalling, even if everything else is equal.
My Levo with a 160mm fork only has 24mm BB drop so it’s on the higher side of things. But having fiddled around a fair bit with the suspension (and I think I’m pretty good at setting up bikes for how I ride), I’ve found myself running 30% sag on the fork and 37% on the shock (which sounds like a massive amount but maybe ebikes like more sag because of the better sprung:unsprung ratios?)
So that’s about 44mm sag front, 56mm sag rear, which equates to about 52mm sag at the BB, so a BB drop of 76mm. And with a 2.4” tyre on the back that works out as somewhere between 290 and 295mm BB height.
With the sag I’m running the mid-stroke is fairly firm so it doesn’t collapse under pumping. There isn’t all that much anti-squat with the power off but it has short cranks which give some clearance. With the power at max it stands a fair bit taller, you can definitely feel it jack up.
Conveniently my hardtail seems to have almost exactly the same pedal clearance as the ride height sits fractionally higher but the cranks are 5mm longer.
I think you get really tuned into pedal clearance if you ride bikes with very similar BB heights. If you usually ride taller bikes and then switch to a low one you’ll take a while to adapt and vice versa.
One more thought – trail centres etc much better suit low BBs than natural trails if you’re going flat out. But I think natural trails and low BBs are fine if you’re not racing. For racing I think slightly higher BBs help you get critical pedal strokes in and give you more margin for error when you’re already on the ragged edge. EWS bikes are rarely super low.