Lava, slime and teleporters ideally shouldn't be transparent. But, well, they are!
r_wateralpha shouldn't ideally have settings. It should be on or off. And something like the automatic water transparency code should be used to detect if it exists. Then again, it does have settings.
I personally don't think r_shadows should have settings, either they are on or they are off. And some particular setting should be "the one".
I guess what I am saying is that Quake is going to be Quake, but a mod or total conversion can make whatever rules it wants.
Adding to the mix: fog in deathmatch maps = no ... unless you are going to do it in software too, otherwise you are putting GL users at an unfair disadvantage. That being said, everyone is probably going to turn fog off --- plus bots do not see fog.
Complicated post, yes? Valid concerns? yes. Kurok doesn't use alpha entities but rather Tomaz alpha textures. Which are superior --- just try to make a door that is glass with a solid metal non-alpha texture for the metal parts of the door = you can't = alpha is all or nothing, either the entity is alpha'd or not.

But using Tomaz alpha textures, you can.
A big tangled ball of a mess.
Part of my message above: unless the map compiler is enforcing that lava is not transparent, an engine that takes advantage of the compiler making it transparent isn't guilty of a crime. This can matter in multiplayer.