The level ordering used does matter, as the mapinfo.txt in the mod expects the retail maps to be named a certain way. As it says in the readme, it assumes the default "Xaser ordering" is what's used. You'll probably get the wrong maps if you use the PSN order.
Does the 25th Anniversary pack just add new music? If so it would be possible to hack in those tracks by editing the mod's mapinfo.txt to point to those new tracks.
The selection skull not being visible in 4:3 seems like it should be a GZDoom bug, ie a long episode name should never cause that. I'll inquire on the ZDoom forums.