Nah, I can see the heels and the base mesh for both the skirted and skirt-less versions. Lemme edit this comment when I get screenshots.
Edit:
So what I did was I took the heels meshgroup from the base mesh with heels and exported it. Then I imported it into the base mesh without heels, imported the heels mesh, moved it into place and chopped the foot off from the CBBE outfit.
For some reason, this breaks the other armor additions? I looked inside Nifskope and found that the .nif Outfit Studio exported was missing the BSConnectPoint nodes. Would that be the