It counters nothing of the sort.
If I say that “all phylogenetic studies to date show that humans and chimps are closer than either is to a gorilla”; you would have to counter that by showing me a phylogenetic study that concludes that humans and chimps are NOT the most closely related primates.
Instead all you did was try to indicate that ‘phylogeny means nothing’ and pointed us to a 10 year old article that didn’t support your contention that phylogenetic data on mammals was somehow suspect.
Or I could show ridiculous relationships in generated phylogenetic trees (like the ones highlighted in the article I linked) and point out that genetics is far from completely understood.