Any mod out there that fixes the issues with the robe/skirt meshes clipping against boots and various footwear/body parts? There are also oddly shaped holes through robes that are stretched in and out whilst running.

Thanks!

Unfortunately, to the best of my knowledge at least, about the only way to accomplish that is one of the following:

1) Giving Morrowind a physics engine.

2) Animating (also known as "physiquing") the robe/skirt/coak/cape/whatever so that they stay out of the way.

3) Building custom meshes made specifically to fit together without clipping.

Obviously the first one is the most difficult (may also be impossible, I wouldn't know), the second considerably less so but still a challenge, and the third is the optimal choice, though it's scope is rather limited because any robes/skirts/cloak/capes/etc. NOT built by the same modder would still most likely clip.

Is there potentially a robe/skirt overhaul out there then that simply widens their circumference so that they don't intersect or interfere with any of the game's leggings/boots/footwear?

Most of the clothes overhauls deal with making them look better. To my knowledge, no one ever really bother addressing the clipping issues with wearing something over ones armor. Probably because most players don't wear anything over their armor. Would be my guess.

This could probably be fixed in the Morrowind Code Patch by turning off character rendering for armor while a robe is being worn and, similarly, turning off rendering for leggings while skirts are being worn, though that one may not work as well.