The important part:
SHUMA and Pugman's answer is close to the botched solution. You'd want Mod 1 to be the one you want to include, Mod 2 to be WXP (if needed) and Mod 3 (or Mod 2 if they're not WXP mods) to be W40K.
In brief, what you want is to edit one of the .module files, add the other mod's name as RequiredMod.1 and add one to the RequiredMod number of the other mods already listed. It won't necessarily work properly with AI and win conditions, but it's as close as you can get without understanding AI and SCAR scripting.