Flatpaks are not meant to replace established package managers, but to act as a supplement to them. Flatapak's design decisions go to huge lengths to ensure they are a side-by-side system with default package managers e.g. the notion that Flatpak packages have a different XDG_CONFIG directory so as not to conflict with applications installed via the main package manager. Therefore the argument that they are harmful to distributions is absurd, as there is no aim to replace your precious "properly" managed dependencies and the option to never opt-in will be always available.