It's funny, I do almost the exact opposite--whenever there is a flatpak version, I prefer it over a built-in apt package. The flatpak is almost always more up-to-date and often has the features and bug fixes I need.
Examples:
- Vorta (0.8.12 flatpak; 0.8.3 apt)
- Pinta (2.1.1 flatpak; 1.6 apt)
- Minder (1.15.6 flatpak; 1.13.1 apt)
- Xournal++ (1.2.1 flatpak; 1.1.1 apt)
.
I don't think it's fair to expect the distro maintainers to be up to date with every software out there--the universe of software has grown and grown, and we just can't expect them to wrap/manage/test every new release and version bump.
The short answer is "yes, but only as much as it needs to". Flatpak had to make a decision between "do we guarantee the app will work, even with system upgrades" or "do we minimize space" and they chose the former. The minimum necessary dependencies will be installed (and shared) amongst flatpaks.
Have you had the unfortunate experience of a utility or program losing its packaged status? It's happened to me before--for example fslint. I don't think this can happen with flatpak.