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If GZDoom v3+ is the best choice for WadSmoosh,
will it work on Zandronum v3+ as a seperate project?

Yes, it should work with Zandronum 3+ but you'll have to make one small change to your doom_complete.pk3: open it up in a ZIP archive editor and remove the file "menudef.txt". This removes the three options menu compat flags WadSmoosh offers, but they shouldn't be necessary.