Admittedly MakeClothes has its limits. But, when viewing the problems you report, I get the impression, that you should get your vertex groups sorted first.
Ok, seems suddenly to fit nicely with the helper 'tight' geometry binding, so I can say you are my savior !
Maybe ask you other tedious thing : If I bring some high heel object in BL, how can I fit them on the helper base human which have no skeleton for this specific pose ?
For high heel boots you might get away with plenty of plenty of vertices in the delete vertex group . Another solution: first model your high heels to a posed base mesh, then rotate the shoes to the rest pose, i.e. sole of foot to ground and run make clothes. As a last step you can add a special pose by editing the mhclo file in a text editor, which is an less documented/undocumented feature.