This is too general description of the way you use. You haven’t even provided any system info.
Are you one of those that don’t care about Rules?
I am not sure this is welcome to the forum… 
Running a flatpak app (not a native archlinux system app) is not always automatic, depending on your DE.
https://wiki.archlinux.org/index.php/Flatpak#Run_applications
https://wiki.archlinux.org/index.php/Flatpak#Adding_Flatpak_.desktop_files_to_your_menu
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