I would say _Pterodactylus_ is indeed the eponym of Neopterodactyloidea, albeit indirectly. Pterodactyloidea takes its name from _Pterodactylus_, and Neopterodactyloidea takes its name from Pterodactyloidea. So I agree with the authors.
Besides, Concilazhia is a much better clade name than Neopterodactyloidea in my opinion.
While on the topic of clade names, I really like the name Serpennata - well-thought-out and very apt: "Portmanteau of the Latin _serpens_ meaning ‘snake’ and ‘pennata’ (fem.) meaning ‘feathered’ (Gaffiot, 1934). ‘Feathered serpents’, in allusion to the extremely long cervical series of azhdarchids in this clade, and to the internal specifier _Quetzalcoatlus_, named for the Aztec deity Quetzalcoatl, depicted as a flying feathered serpent."
Finally (and unrelated to clade names) - am I correct in interpreting that _‘Palaeornis’ cliftii_ is now regarded as a valid species of pterosaur? I mean in a diagnostic sense. The genus name is obviously preoccupied. I had wondered if 'Paleornithis' is available - Mantell mentions the name after he realized that his _Palaeornis_ was preoccupied, but before he accepted _P. cliftii_ was a pterosaur and not a bird. But after reading Witton et al. (2009), the status of the name 'Palaeornithis_ appears to be too ambiguous.