Hi
For the shoes "hide faces under clothes" should be used. Same goes for the pants, skin bleeds through. So it should be exported without the skin under the clothes. The reason for bleeding through is simply mathematical:
http://www.makehumancommunity.org/wiki/Documentation:MakeClothes_Delete-GroupsThe standard shoes should not bend like the foot. Afaik they are designed like that. So the sole is made stiff and it follows a few vertices of the foot (looks like the toe-box region). It also depends on the skeleton (game engine, default whatever) The animation (I guess) deforms the foot itself, which normally has a foot and at least one toe-bone.
So best to export with delete vertices or try some of the shoes from the user asset repository. They partly are able to deform in a way which might be wrong in reality but correct if you need the skin under the shoes, because not all are made the same way.
Btw.: Most closed heels are deleting the foot itself because it would peek through in front.
Greetings
Punkduck