I don't think anyone who actually *knows* anything about avian
systematics ever seriously believed that Passeriformes is the
sister-group to all other extant birds.
I don't think anyone who actually knows anything about mammalian comparative
anatomy ever seriously believed that Rodentia is paraphyletic to the rest of
Reptilia. I must conclude, therefore, that the mol. phylo. people who
honestly did believe this did _not_ actually know anything about mammalian
comparative anatomy. I don't have a paper handy, but I've read some quite
surprising wordings about how morphologists should seriously consider this
exciting phylogenetic hypothesis.