The visual bug is described in more detail in
this thread I started on NexusMods. There are more images there.
Basically the mesh DLC01IdealMasterCrystal.nif doesn't show up properly in-game or even in the CK64, but it looks perfectly fine when opened in Nifskope.
Even the oldrim version of the mesh renders the same (badly) in SE, despite looking fine in Oldrim, so it's something in the way SE handles the mesh.
I made sure to confirm that I have zero mods that affect the mesh or textures, and I tried to get some confirmation of the issue before posting here; although only two people replied but they did confirm the issue.