1. This question falls under the "why don't you add WadSmoosh support for [random free mod that you can just download and load in like any other mod]?" section of the WadSmoosh FAQ - because WadSmoosh is for packaging up retail content only.
2. The point of Master Levels Menu Interface is that you can jump into any level at random. The point of this mod is that the levels have been placed into a deliberate sequence that establishes them in the context of their authors' other work. These ideas are incompatible.