I'm sorry, but that's exactly what I said. It seems I'm not coming across correctly sometimes. I apologize.
The thing is there is a body "inside" each clothing item. Your respective bodyparts will get "replaced" by the one you just equipped. If you wear a Vanilla item without having it replaced with a fitting one beforehand, you effectively have a Vanilla body wherever it's showing through. So it was a gap in the body "coming with the shirt". That's nothing the body mod could fix ever and it is why I think those Stock Replacers should rather be mentioned as "required" instead of just "recommended". Clothing and Armor is effectively nullifying the effect of a body mod for the bodypart underneath.

Oh, I see. I assumed that if you weren't using equipment replaces, the body would just clip through the clothes. Thanks for the information, that makes a lot more sense.

Drake, if you are still looking here, I seem to recall a similr question (maybe I even posted it and you answered it ) that the body texture is used for the skin showing in an armor replacer. I assume this is not the same as the "body part", but rather the skin texture shown itself.

Yes, and that's yet another cause for issues when not using Stock Replacers or wearing an item not meant for the respective body. The bodypart's "meshes" come with the item that is worn, while the body textures are assigned on a per-race basis. Different body mods/bodies use different texture mapping layouts and mostly none will fit the others. Now your race using textures for one specific body while your item includes meshes for another they will no longer fit and cause such anomalies like "nipbles on the arms" (wrong textures), or what it is that is to be read complained about on a regular basis, or even missing textures (purple) or normalmaps (pitch black or invisible, sometimes even eliminating the mesh's rigging I experienced) when it's a custom race without textures for the bodyparts the body included in the item requires. (For example Robert's bodies only use and need 1 single texture file, the foot one, for the whole body. Custom races done for Robert's often only include this 1 file. Now wearing an item with a Vanilla body mesh inside, Vanilla needs 1 seperate texture file per bodypart, thus 3 of 4 bodyparts will effectively be missing their textures.)

From a technical point of view, to make a bodypart mesh inside an item use the race's textures it needs to be using material "skin" and the NiTriStrips/Shapes have to be "named" according to the texture slot it should be using ("upperbody"/"arms", "lowerbody", "hand", "foot"). Then every texture information given in the NIF file will be ignored by the game engine and overridden with the settings from the race and the skin tint and color set during CharGen. Well, all but the fact that when there's a file assigned in the NIF which is missing you'll still get a "missing normalmap"-issue, although the game will never use the texture assigned when it's not missing. I found out about those facts the hard way quite some time ago.

Appreciate the answer. Body textures and mods are harder than installing FCOM