Basically, all vanilla art files, Master and critter.dat, are saved as .frm and the serverside protos call for a .frm. There is no way to add transparency to a .frm, it would first need to be converted into .png with a textfile, a .fofrm added which takes are of the offset.
In order to add transparency to walls by exchanging files, we would first have to repack all of the (copyrighted) fallout files as pngs. As you can see it's not just a lot of legwork but also questionable.
Another option might be tinkering with the "egg", which is the transparent egg-shaped area you get when you stand behind walls. Koniko would have some more info on it, iirc it's a file in the client that you can make bigger to increase egg size. I dont know if it's possible to make a half transparent egg and then make that really big.
Finally, I cant say much about scripting a transparency for walls like the ~roof command but as you can see here it's sadly not as easy as replacing some wall files.