yes and no, I'll very lightly push back on this in the sense that.. it's more like flatpak makes "get it from the source" so simple that getting your software from a distro's upstream does not need to be the default (and shouldn't be the default for many situations).
But, I still see some value in a future flatpak world for bundlers to maintain separate repos where they patch flatpak apps or keep dependencies up to date or change defaults.