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]: