Something you *REALLY* must change to conform to standards:
Use the Half-Life standard for alpha masked textures (see this
http://www.egir.dk/index.php?page=wal_t ... arent.html )
1. You must prefix these textures with "{" so "metal_rail" needs to be "{metal_rail" [Half-Life standard as the way Valve did things.]
2. In your WAD3 textures, you need to set the color 255 like in the above link. [Half-Life standard as the way Valve did things.]
Now ... you are probably saying "DarkPlaces uses whatever alpha is in external textures".
This is evil incarnate for most non-DarkPlaces engines and definitely for the mild set of changes I tried to do here. A surface in a game shouldn't rely on an external texture alpha channel. If I want to cheat, all I need to do is edit the external texture for a door and suddenly I have a fence texture door. And I didn't even have to attempt to edit a map.
I was thinking of making it do this anyway, but if I do it just destroys all ideas for any kinds of standards. I won't claim to know how this works in Quake 3 or other games, and while adding alpha texture support to Quake is in its own way "creating a new standard" ... but I have been sticking to the Half-Life map as it is known.
(* DarkPlaces is a modder convenience engine has its own set of goals. And that's ok for DarkPlaces.)