From a distro support perspective, flatpak is great cause you don’t have to do anything for more packages. From a user perspective it will nullify the advantages of CL. The main reason cited for using it as a desktop is for the performance benefits (to offset the disadvantages). Packages are built by default with westmere (sse4.2) and a few extra flags and a few places with extra libs optimized with AVX2/512 where generic 64 bit Linux is back on sse2.
If you use a flatpak, you forfeit all of that and are using the generic unoptimized packages that flatpak provides. May as well go elsewhere at that point.
Also lets not rely on Phoronix to determine the performance difference between distros. Many of the tests don’t even test the distribution (i.e. what you download from the package manager) and are just flung together with zero thought to pump out another article for ad views.