Thank you both. Indeed, I did not have repo in my user local directory. I figured out that (sorry for not doing my homework
). I added repo with,
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo --user
Same for fedora repo. Issue resolved.
Still, as a normal user, I would have liked that I only install repo once, not have a separate repo for user and system and be able to install using --user option.