Yup, the mod manager was integrated into the game.
However how could the dev go around integrating specific mods into the game?
Like, how you mention the big booba mod, integrating that one on its own would cause issues - Would the dev just take the mod as-is and integrate it? Would he integrate it but change the art? Would he go, hire the modder and make it so that the modder would work on that part of the game? Would he completely ignore the mod and just implement the additional art + mechanics himself?
Because all of those options have their negatives, and would apply to virtually any other mod (increased workload on the game, the need to have more people if so OR more workload on one person, rights issues, selective implementation, questionable implementation, more workload on modders, etc.). Pretty much the same issues with Skyrim modding, where some mods are pretty much needed but don't get implemented, but then others get implemented despite not being wanted at all, or being implemented badly, or when implemented they are outright stolen from the modders themselves.