It is? And you imagine that what is a better model now? That none of the yeast have any common ancestry but spontaneously popped into existence?
Furthermore, I’m not quite sure why earlier attempts with conflicting phylogenetic relationships is a problem at all. As the authors note there are “complex evolutionary events, such as deletion, insertion, duplication, and whole genome duplication”- and so that makes the entire field very challenging. So the more recent paper simply demonstrates that our methods have improved and we have an even more accurate tree for yeast than we ever have before. But somehow you interpret this to mean that the entire premise of building a tree from common descent is hopeless. Perhaps if newer models and methods completely overturned all previous phylogeny‘s then we would have something to talk about… But as I’m sure you’re aware despite tweaks here and there- the major relationships are unmoved. This was a big chance to falsify common descent with cladograms from morphology being completely at odds with genetic and molecular ones- but alas besides some reshuffling hasn’t changed much!