Nickruig, the module-level selection will be going away eventually, replaced with game type and mod selection. The player will have to select a game type, which will select the module defining the game type and all its dependencies. The player would optionally select mods. In the mean time the module selection screen provides rough modding support, so removing it would be a step backwards in my mind.
Ignoring that... I think it would be simpler just to set what modules you want to have mandatory than merge all of them into one.