What happens if I don’t specify the remote? In which order does it search for the flatpak? If it doesn’t find the flatpak in the first remote, does it just move on to the next?
You can give this a try and see. There are quite a few applications present in both (e.g. org.inkscape.Inkscape). Flatpak will prompt which one to choose. Actually it also prompts when you forget to specify the remote, and it finds a matching app in one of the configured remotes.
I used inkscape as an example application that is present in both Fedora & Flathub flatpak repos. You can try installing it without the repo specified, and see the prompt for yourself rather than someone here trying to describe it to you.
# flatpak install org.inkscape.Inkscape
E.g., if you try this, you should get a prompt asking you to choose between the two repos.
PS: Inkscape is a really nice application for drawing vector graphics.
Thanks, all. I tried the Inkscape flatpack that fatka suggested as a test of how it works and it did, indeed, prompt for me to choose:
flatpak install org.inkscape.Inkscape
Looking for matches…
Remotes found with refs similar to ‘org.inkscape.Inkscape’:
1) ‘fedora’ (system)
2) ‘flathub’ (system)
Which do you want to use (0 to abort)? [0-2]: