Will this only work for Silva and UNITE? Could someone use a foundation tree built with some COI database with ITS sequences from UNITE? Or something like that?

How is the consensus taxonomy determined?

Is there a precedent for grafting terminal clades onto the tips of a "foundation" tree like this? If not, I think this approach warrants some validation with respect to the accuracy of the ghost-tree.

Is there a whole genome phylogeny of the fungi available, or a well-resolved phylogeny of a subset of the fungi? If so, you could pull just those taxa out of Silva and UNITE, and use them to see...