The Nature News and Views reported that others disagree that these findings indicate ctenophores are the oldest group.
This is a great piece of work and well done article in Nature by the (mainly) Florida group.
Hard to say what “gummed up” means but the findings are extremely unexpected and makes evolutionary relationships and descent much less understood.
The position of the ctenophores has been debated for several years. I don't know why you say the results are completely unexpected. From Wiki:
The relationship of ctenophores to the rest of Metazoa is very important to our understanding of the early evolution of animals and the origin of multicellularity. It has been the focus of debate for many years. Ctenophores have been purported to be the sister lineage to the Bilateria,[48][49] sister to the Cnidaria,[50][51][52][53] sister to Cnidaria, Placozoa and Bilateria,[54][55][56] and sister to all other animal phyla.[57][58] A series of studies that looked at the presence and absence of members of gene families and signalling pathways (e.g., homeoboxes, nuclear receptors, the Wnt signaling pathway, and sodium channels) showed evidence congruent with the latter two scenarios, that ctenophores are either sister to Cnidaria, Placozoa and Bilateria or sister to all other animal phyla.[59][60][61][62] A more recent study comparing the sequenced genome of the ctenophore Mnemiopsis leidyi with other sequenced animal genomes showed multiple lines of evidence supporting ctenophores as the sister lineage to all other animals.[63] This position suggests that neural and muscle cell types were either lost in major animal lineages (e.g., Porifera) or that they evolved independently in the ctenophore lineage.[63] Ctenophores and sponges are also the only known animal phyla that lacks any true hox genes.[64]makes evolutionary relationships and descent much less understood.
In general, or only concerning ctenophores? I'm not sure I agree in either case.