I picked up 4 again for a bit and grabbed your 3 Morningstar outfits from the Steam workshop, I am on the legacy build.
I've run into two clipping issues with the boots, both are on the upper leg/thigh. The first one seems that I just can't find any version of the weight triangle that has no or minimal clipping in that area. I usually use a macular body, I had a table edit for giving more range but even after replacing with a default table it still had some clipping. It seemed less severe on a neutral weight triangle, but even a full 0 triangle there was some noticeable clipping.
The other (which lead me towards just accepting it) is that it seems that many ways to swap the boots don't morph the upper leg, leaving a hard cut from the leg to that lower leg that usually is covered by shoes. Given how there are no over the knee boots in the game this makes me thing there is some sort of engine issue that may have been broken in one of the later patches.
Could it be an issue with the steam workshop or one of the newer patches? I figured I ask since you have replied recently and I don't have a easy way for a full fresh game install currently.