The way I have my custom skeleton set up, the crossbows are stuck halfway into the character's shoulder blade. I'd like to push it out without changing the bow location which means working with the weapon, not the humanoid skeleton. Is there anything I can do in Nifskope to the weapon to separate it from the body when slung on the back? I have a feeling the answer is no, but I have to ask.

Unfortunately, no. It's all about the bone.

You can slightly adjust the weapon position on ArmorAddon records, using the Weapon Adjust field, but if it's happening on every single armor type that might not be practical.

As a matter of fact Hanaisse I've done extensive modding on many of the ArmorAddon records to push the weapons away from the body (even before Dawnguard came out) because I felt the weapons clipped into the hip on a lot of pieces. But that hasn't helped with these crossbows.

As a matter of fact, the crossbows are very strange in the way they act. If you add the line bDisableGearedUp = 0 to skyrim.ini and hot key a crossbow and a sword so they both show up, you'll see what I mean. When the crossbow is equipped, the sword clips far into the hip. When the crossbow is unequipped, the sword pops back out to its normal position. This behavior is independent of the ArmorAddon figure and must be something the weapon itself is doing. I noticed a lot of files in the dlc folder accompanying the crossbow.nif that had to do with the skeleton, but they weren't nif files. I don't know what they were, but they must be governing the way weapons are positioned when the crossbow is equipped.

At this point I have half a mind to to just resize the WeaponBow bone to 0.0001 (out of sight out of mind), but I don't want to lose the look of the regular bow on the back, which I was finally able to position beautifully after a long time of trial and error.