So I just tested this again with an accomplice that has near perfect hearing and certainly better hearing than mine. The difference was confirmed - so I can (hopefully) rule out madness on my part.
Using my daily driver EBMM Cutlass the difference was easily noticeable. At 100% much fuller and more lush sounding on the neck pickup than when sensitivity was set to 50%. Remember, I can only fully light the amber input light with this guitar - it's not possible to tickle the red.
Next up... Suhr Classic S on the neck pickup: There is much less noticeable change. Only a slight difference but much more subtle. Nothing that I would bother worrying about. I would be happy using 50% or 100% with this guitar, as others have said - it just doesn't matter.
So here's the thing. The Cutlass has a bufferred output. The guitar takes a battery. The Suhr has regular traditional pickups.
Another interesting point: I also used to have the same Fishman Fluence Tele pickups as
@paisleywookiee and it's interesting to note that they are not quite like active pickups, but they are also not "normal" pickups and are battery powered. I don't know if the output from the Fishman's is buffered, but I guess it could be?
It could be significant that both Wookie and I aren't sending regular guitar output signals when we notice these differences.