Thanks for the long story.
Ok, the long term fix would be to bypass ffmpeg whenever possible and rely more on fftw3, so that it doesn't break compatibility with zita-convolver?
And this would in turn requires fftw3 to have a Thread Safe Planner as per https://github.com/FFTW/fftw3/issues/16
-> according to the release notes the implementation in fftw 3.3.5 was broken and this is apparently fixed in 3.3.6 (current version in Arch.)
Did I get it correctly?
Anyway, Guitarix works fine for me with the changes you've done: the volume is now consistent between 44.1 and 96k (at least for simple presets - I didn't compare all modules).
But users running at 44.1kz & 48K will probably be less than happy that their their presets have a high chance of being too loud.
This would probably require a word of warning if you plan a new release in the current state...