Follow system theme is a great option to switch between light and dark appearance. But if the app is installed via Flatpak it will never know about system setting until the application intentionally support it. My suggestion is to make application support flatpak fully and so that it can read system setting for light/dark theme option.
This is a limitation that’s common among Electron applications. For example, applications like Discord don’t automatically set the header bar to match the system theme under Wayland.
Upon further inspection, it doesn’t even look like Obsidian can determine whether to use light mode or dark mode even when being run as an AppImage on Xwayland:
@shvedchenko Please file a bug with upstream Electron if you can.
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