you're right, the darkness in that underwater section seems about the same. I guess its just above water where the light seemed a bit different.
This Is quakespasm on the left with mid brightness, and your video on the left - you mentioned youtube darkening somewhat, so this will probably be a factor.
I do remember opening original quake in dosbox recently and remarking how much darker it looked, and have since adjusted my quakespasm brightness down a little to match.
Cheers for the videos, I've linked them to the QUMP crew and we'll keep an eye on your channel!