A little-known feature of MakeClothes is that you can tell MakeHuman to hide surfaces which are located beneath the clothing. This prevents the poke-through glitch you can see when using other character deforms than what you modeled on.
All that's needed is that you select (on the human, not on the clothes) all vertices that are completely hidden by your clothes, and assign them to the "delete" vertex group before you make your makeclothes export.
It's usually best to be conservative when selecting what vertices to hide, so that you don't see a hole in the body from some extreme angles.