Thank you for answering! I'm using Proton, and have added those in launch options. Without them (at least ddraw) the game would launch into Fallout 2 instead of 1, so I'm pretty sure they work.Make sure you've added draw.dll and f2_res.dll (both native and builtin) in winecfg DLL overrides. I don't recall having to do tinker with any file names since Windows doesn't care about case.
I'll try to retrace your steps. Did you run undat.sh to extract the files?
I thought it only didn't on case-insensitive filesystems, but after some googling it seems you're right: Wine finds the right files for us. Though there might be some bugs in that.since Windows doesn't care about case.
In my data folder there are some duplicate subfolders like "sound" (which came from the mod archive) and "SOUND" (which was unpacked from master.dat). Is that the case for you too?