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When you define your own desktop files e.g. under ~/.local/share/applications for example for Ungoogled-Chromium like this:

[Desktop Entry]
Name=Ungoogled Chromium
Comment=Privacy friendly chromium edition
Exec=flatpak run com.github.Eloston.UngoogledChromium @@ %u @@

If you want to properly open an url in any given context of your os, you need to prepend the exec in the desktop file with @@ %u @@ to parametrize it with the given url. So the xdg-* tools can retrieve the url and delegate it to the defined default browser.