Fennec enables access to about:config, so making all of arkenfox's changes manually(by viewing its user.js and toggling it in about:config accordingly) would also be an option, none of arken's toggles are desktop only as far as I know
Tzeentch
You can take a crack at using Geddit I suppose, doesn't use the reddit api so should keep working, but is in turn kinda janky as a result: https://github.com/kaangiray26/geddit-app
The themes section on the desktop integration doc here might be of use: https://docs.flatpak.org/en/latest/desktop-integration.html
This may be useful for further elaboration: https://www.reddit.com/r/flatpak/comments/y9jmqj/the_general_flatpak_qt_and_gtk_theming_guide/
Going off of these guides my best guess would be that you don't yet have kvantum or some other theme runtime installed within flatpak
I'll also mention Stylepack exists for automating and streamlining theme installation, it's only for GTK currently however but maybe will be of use in future: https://github.com/refi64/stylepak
There's a few options
Newpipe, uses it's own extractor, also can act as a player for SoundCloud and Peertube, there's also a fork with SponsorBlock: https://newpipe.net/
Libretube, uses the Piped api, generally seen as the one with the best UI: https://github.com/libre-tube/LibreTube
Clipious, uses the Invidious api: https://github.com/lamarios/clipious
Could also watch videos in a browser from an Invidious or Piped instance I guess
And while I'm at it I'll also mention there's a client option on desktop too, Freetube: https://freetubeapp.io/