It peaked at 4.05% in March. The last 2 months it went just below 4% as the Unknown category increased. For June the reverse happened, so 4.04% seems to be the real current share of Linux on Desktop as desktop clients were read properly/werent spoofed.
Yes, Flatpak fixed a lot of the old shenanigans we used to have when everything was either native package, or a binary to hope for the best and install libraries manually, or source code to collect everything that’s needed for building and again, hope for the best. It is however designed to provide a way to install graphical apps, but can’t handle everything native package does (like out-of-tree kernel modules, CLI utils, system services)
I believe it can do CLI, but that’s not always been the case and not a lot of CLI apps adopted it as a result
But for most of what the typical user, or even a lot of what a technical user, needs, it does a good job