Thanks for posting about this! I never thought to try this as an Akregator user, but it’s a great idea… I spent the past day getting this to work since I also use the Flatpaks; hope it helps.
As suggested by @progandy, one solution is to define a custom protocol where the URL gets passed to a script that opens Firefox Reader with the URL; here’s what I’ve done:
Decide on a protocol name, which the URL will be prefixed with and passed to xdg-open since that should be available to the Flatpak. I used firefox-reader as the protocol, so I put xdg-open firefox-reader://%u as the custom command (so a command Akregator would run might look like xdg-open firefox-reader://https://example.com).
Define a desktop entry to support the custom protocol (you can see mine below). ~/.local/share/applications is the standard place to put these, as far as I’m aware. Since the custom protocol needs to be removed from the URL, I wrote a script (also below) to do this and then call Firefox with about:reader?url= prefixed. The script can be anywhere in $PATH.
Add the desktop entry as a “default application” for opening URLs using this custom protocol. In my case, I ran xdg-mime default org.mozilla.firefox.reader.desktop x-scheme-handler/firefox-reader (org.mozilla.firefox.reader.desktop is the name of my desktop entry file).
You also might have to update some mime/xdg database stuff. I had to run update-desktop-database ~/.local/share/applications so xdg-open would find the “Firefox Reader” desktop entry.
open-firefox-reader.sh scriptbash #!/usr/bin/env bash flatpak run --user org.mozilla.firefox about:reader?url=“${1#firefox-reader://}”
If you have any other trouble or want to find more information about this since the desktop entry could probably be tweaked, here are the sources of note I used to figure this out (If I forgot a step or two writing this, they should also be present somewhere in there):