Thanks for all the tips.
Here’s a solution that worked in the past -- it describes how DPI settings get set in fonconfig to 96 dpi, instead of 1200 (the lilypond default):
My fontconfig already has it set to 96. I have another machine with the same operative system and general settings, equally up to date, and there, lilypond works fine (they are not a perfect mirror of each other).
To clarify my situation, anything I compile has that error, even if the version declared is the current one, and the failure happens from both frescobaldi and the command line.