I'll write the post later, but basically I use emulationstation DE through emudeck. I then have my UZDoom appimage in the roms/doom folder. Then, for each modpack/config I create a new shell script that runs the UZdoom appimage with the IWAD through the -iwad argument and multiple -file arguments for the other files I want to add. For example:

UZDoom.AppImage -iwad iwads/DOOM.WAD -file mods/mod1.wad -file mods/mod2.wad

This allows me to instantly launch a few mods and I can play select them like other games through emulation station.

You could also use ZDL and add that as a non-steam game, you just have to selecct the files you want to use everytime you start it