i have noticed a lot of issues with clipping and miss aliened genitals plus the new npc spawn naked not sure if there post to be naked,
tho normal default npc's are having no issues but custom npc's are have many issues with animations with clipping and miss aliment issues.
question have you tried using loading NPC's without giving them armor or weapons ? the NPC in the two pictures above the red one was put into the game by mistake without being given armor or weapons...i just wiped my NPC folder and redid each NPC giving them armor and they seem to be fixed this is the same large NPC and my player charcter now with the NPC given armor and a weapon and no the NPC is not an edited file just max height and some other high sliders
I just flat out didn't even see the option to add clothes the first few times i added the npc's i thought they would just be given random clothes and some sort of weapon, but seeing now that you can give them things is pretty cool, i guess i found out the hard way the NPC's need everything added to them or they break.