prboom seems to be unable to 'see' the IWAD in the same directory of the currently loaded PWAD.
Unlike the Windows version of RetroArch, where PWAD and IWAD can be organized within folders, Linux seems to require the IWAD to be stored in the system folder of RetroArch.
If both Doom2.wad and Doom1.wad are in the system folder, the Doom2.wad is always used, causing PWADs that require Doom1.wad to crash, such as Sigil.
There's no way to run both, only Doom2 PWADs seem to work.