This is really a big issue. The solution in MakeHuman is pretty complex but works pretty good. I do not see the problem in MakeHuman now.
For the body, of course it makes not much sense to make all 1000 shapekeys/morphs available to a game over Blender. Conan Exiles and another have just one or two on character creation (plus overall scaling). Since shapekeys are based on linear mapping of vertices offsets, a combination of offsets seems to be still commutative.
Wouldn't it be easier to create such addional shapekeys in blender based on differences of MHX2 output with a base reference? In the documents there is a warning it may not work with animations, but maybe this can solved?! This seems to be existing functionality in MakeHuman and Blender. Is there a tutorial missing?
A solution for clothes would be required on top, maybe easier to enhance clothes in blender regardless of the source of mesh.