I wonder what is the difference between installation from fedora APP interface and the coresponding dnf installation?
I installed Geany from APP interface in order to use it as my LaTex editor. Not only it is unable to detect the installed texlive and compile the .tex file, when I do geany --version in terminal it can neither detect the installed Geany.
You probably installed the Flatpak? Try flatpak history in a terminal to confirm.
Generally the app stores (GNOME Software, Discover) etc allow you to choose whether to install the rpm or the Flatpak, though the difference between rpm and Flatpak in the UI can be non-obvious.