I know that the dark mode setting is disabled by Resist Fingerprinting. I am not using that, I am using the Dark Reader extension. The extension still doesn't work, but it works on Firefox.
Other extensions I have installed: Ublock Origin, Decentraleyes, Skip Redirect, Onetab, Old Reddit Redirect
Create a new profile, install Dark Reader extension and see how that goes ?
/var/lib/flatpak/exports/bin/io.gitlab.librewolf-community -P (Remember to use the same command to switch back to your current profile, or choose to make it ask every time)