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.