(This is going to be grossly oversimplified and possibly minorly inaccurate, but) Flatpaks are built against and run using shared runtimes, so if two Flatpaks share the same basic dependencies (and those dependencies are included in the most common runtimes, which they usually are), you only have to download the shared runtime once. Every Flatpak built on the same runtime will share the one runtime. The way you described it is a common misconception.
Now if the packager manually bundles less common dependencies into the app itself, yes, that would have to be individually updated, but that’s theoretically more of an edge case.