in other browsers that send computer preferences, dark mode is enabled (because dark mode is on in my settings). But librewolf blocks that. Is there a way to manually toggle dark mode on the flathub website?
that is more of a librewolf settings issue
In LibreWolf’s settings, under “privacy and security,” disable resist fingerprinting. Then go to the “appearance” tab of LW settings, and you should have the option to set your theme to dark mode or to follow your system theme.
At that point Flathub should be able to detect that your browser prefers dark mode.