While waiting for that person you quoted to answer you, I take the liberty of saying something. It would seem that even if Freedoom is an Iwad, it should be considered, during the conversion to .gba rom, as any Pwad, as already suggested by a previous user:
"Here's how to do it / what I did:
1: Make a duplicate of freedoom1.wad. I renamed the duplicate to freedoom12L.wad, so I will be referring to it as that.
2: Open freedoom12L.wad in a text editor. Change the first letter from uppercase "I" to uppercase "P." The beginning should now read: PWAD
3: Open freedoom12L.wad in a Doom editor. I used SLADE. Rename all the tags in E#M# format to MAP## format. The first one should be called MAP01, then MAP02... all the way down to MAP36.
4: Save the file and close the Doom editor.
5: Open it in the text editor, again. change "P" back to "I." The beginning should now read: IWAD
It should now work with the GBA compiler.
Another thing to take note of is that the when you use the GbaWadUtil, do not copy the freedoom12L.wad.c as soon as it appears. Instead, wait until the command window returns with the prompt for you to type another command. Usually, this looks line "C:\devkitPro\projects\GBADoom-master\GbaWadUtil>", with a flashing underscore after it. You can then close the GbaWadUtil."
I apologize if what I wrote did not answer your question.
P.S. I remind you that only up to v. 0.10.1 is PrBoom compatible; the most recent is not and crashes at some point.
Greetings.