That tends to wave away the responsibilities of the distributor.
The distributor's job is to package software. In effect, putting it in their repo is sort of vouching for it-- they know it's going to work properly with the rest of the repo, and be built with whatever standards the distribution offers (i. e. Debian being sensitive to IP concerns, Clear Linux doing its shiny performance optimizations, etc.)
If you just hand everything off to external self-contained images, you lose a lot of that.
I suppose you could do 'captive' collections of Flatpaks, designed to meet the same optimization and compatibility promises, but at that point, you have RPMs with extra steps.
Taken to an extreme, a Flatpak-centric distribution ends up looking a lot like Windows, where there's no useful tools on the distribution media and a new install is followed by hours of clicking through third-party installers (or permissions consent dialogue boxes maybe) or devolving trust to scripts that promise to do it for you.
To an extent, I also just resent the entire "it works on your machine? We'll ship your machine" mentality-- Docker/Kubernetes and Flatpaks/Snaps are sort of variations on the same theme. They come from a mindset of infinite free resources-- the disc space for all those redundant dependencies is coming from somewhere-- and it would seem to make brittle, hacky code more viable because you don't have to FIX code that depends on unguaranteed aspects of an API contract.