It seems like all of these questions are answered in the article? Hell, they've even got a geneticist working on sequencing the genome of the dormant yeast they

It seems like all of these questions are answered in the article? Hell, they've even got a geneticist working on sequencing the genome of the dormant yeast they extracted from the ancient pottery, so once that's finished I think we'll know pretty conclusively what we're looking at. But that the yeast would only grow when fed emmer flour, not modern wheat flour, already seems to suggest that something unusual is going on here that you wouldn't be seeing if it were truly modern bread yeast.