Few years down the line, the problem still persists. I have distributed my foliage, made some changes to the lightmaps, reimported and now I have plenty of unused empty material slots, which I can neither get rid of, nor populate with a material. In order to fix that, I’ll now have to delete ALL foliage from my level, delete the mesh from content browser, reimport, setup LODs and their distances and populate the level back again.
Incredible workflow!