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.