I couldn’t leave it alone… it’s definitely the API conflict. If I remove the fonts from the system profiles area, then the fonts in the /Dropbox/Apps/Scrivener/Fonts folder are available from the Scrivener font menu. Of course they then disappear from Pages, which evidently (and unsurprisingly) uses the new font API.
It’s no hardship to avoid Pages, but I miss having the fonts just available in Scrivener, Ulysses, Office Suite, and iThoughts. I was confused by the fact that I’d installed the fonts via both methods, but I prefer having them installed iOS-wide.