Certain costumes for male characters do not cut underwear.
If you export those costumes to aprtcutdesc.xml and add underwear cut to the relation item, the penis will not appear.

Stockings like Ranger's Gotha Rensa are transparent.
There is no partcut effect attached to these.
So why does the body clip?
The answer is simple.
My nude bodies are skin weighted.
If I add the original skin weight, the body with the added pussy will deform and distort the pussy when the character spreads her legs.
I have modified the skin cluster around the crotch area to eliminate that distortion.
This means that the body clips because the skin cluster is different from the crotch area of the costume.
The problem does not occur in my skimpy costume because I have removed the costume from the crotch area, but it is not suitable for people like you who want to display a nude body only when the character's costume is removed.
The best recommendation is to use the default body and a DDS file with a picture of Pussy in the nude.
I do not intend to modify the polygon mesh of every character's costume.
Because it is easier to have the characters undressed.
P.S.: See if you can also use parthidedesc.xml if necessary.