full body female mesh has skin box shape

Hi. You started a package from yfBody_CocktailStrap, which is split into 3 meshgroups to interact with shoes.
Your blend contains 1 meshgroup, so only one is replaced while others stay

Filter the catalog by one meshgroup and start a package from a different item


Unrelated issues:
- when modeling in MD, set mesh type to Quads, the garment will look smoother;
- when exporting from MD, dont include internal shapes, you dont need them;
- when closing holes, either Extrude and Collapse, or just press F to close;
- after closing a hole; unwrap it;
- after transferring weights, use Limit total;
- vertex paint can be transferred.