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You should be able to make a WadSmoosh-compatible version of plutmidi.wad by renaming all the lumps inside to P_TRACK instead of D_TRACK.

What WadSmoosh produces is an IWAD, PK3 just denotes the format used (ZIP instead of the classic WAD format).

Much of what WadSmoosh does, with regard to defining custom episodes, intermission screens, and texture replacements is due to ZDoom functionality that most source ports don't have. If there's a source port that has equivalent features (maybe Eternity?) and someone wanted to make a fork (not a branch) of WadSmoosh that produced an all-in-one IWAD for that, they'd be welcome to - WadSmoosh's code is released under an MIT open source license - but I only use GZDoom so that's all I'm willing to support. 

That makes sense. Anyway, the point I was attempting to make stems from wanting (near) universal compatibility with this. No PK3 format, since many source ports can't handle the zip format, or Mapinfo, since that would be the job of the sourceport. But, if that isn't your goal, then that's just the way it is.

However, do you think that future versions could add in device-exclusive official maps? Sush as by extracting the maps from the GBA ROM and PSX ISO? That's st least in-line with the goal of the project. 

PSX, GBA, Jaguar etc versions of maps already exist as freely available (painstakingly manually reverse engineered, as I understand it) PWADs, so I'd say just run those as mods.