Apps coming from different packages will have conflicting .desktop files
I do not know if there is a fix for this but imagine you install the app X from the repos. You rename it. A .desktop file is being created in .local/share/applications. You now install the same X app as flatpak. The desktop file will have the same name. So when you search for the flatpak app in Whisker or AppFinder you'll only find the repo one because the .local/share/applications has priority.
Even worse you uninstall the repo app and now you have a dead X app in your menus because it reads from .local/share/applications and there it can only see the .desktop file for the X app installed from the repos. Thus you cannot find your flatpak app anywhere.
I know this is an edge case, kinda, but nowadays it happens that many times people use different packaging repos and it will conflict with each other.
Even if you do not rename the X app, if you install the same app as flatpak and from repos, you'll only have 1 entry in the menus depending what you installed first probably.
Is there a way to label the flatpak apps with a (flatpak) in the desktop file?