Most Flatpaks depend on the Freedesktop Platform runtime, or GNOME/KDE runtimes, which are derived from it. This contains several hundred common dependencies and librarires programs need, like gcc and python. When you update the runtime (change it from 22.08 to 23.08 in the manifest), all the dependencies are updated too. Many simple applications don’t depend on many more dependencies than are available in the runtime. Some…have more complicated dependency trees.
But counterpoint: the developer will update the dependencies when they are known to work properly with the application. Upgrading GTK3 to GTK4 in the GIMP flatpak will just break the application. Same thing with Krita and the dozens of patches to libraries it depends on. If you upgrade the application in the name of security before it’s compatible, all you end up with is a broken application. Which I guess is more secure, but that’s not helpful to anyone.