Synaptic is aware only of deb packages. Synaptic does not maintain it's own package database - it uses the same apt and dpkg database used by apt, aptitude, dpkg, and other deb-based managers. If you install a deb package using any of these tools, you can uninstall it using any other of these tools.
Synaptic (nor any other apt-based application) cannot detect flatpacks, snaps, pips, wheels, compiled, or any other type of package or method of installing...since those are not deb packages.
Ubuntu does not have any single application that can see all the possible methods of installing software. In this open-source environment, somebody can add a whole new method tomorrow without checking with any gatekeeper. It's up to you, the user, to keep track of the methods you use to install and to use the appropriate tool for that method.
sudo apt-get install gimp
or what? I suspect that you installed a version outside of the official Ubuntu repositories, yes?