Debian and Arch are exceptions. I believe maintainers of every other mainstream distro are exploring immutable distros or at least shipping confined apps.
That is no longer the case with the new default Desktop subiquity installer in 23.04. Instead of a single squashfs, there are separate squashfs files so the minimal install is faster than default in 23.04.
Why can't Ubuntu ship some extensions by default? After all, Red Hat Enterprise Linux ships GNOME Classic which is GNOME Shell with some extensions and a tweaked theme.
Windows 10 will have it next week in the Creators Update. Android has it in 7 "Nougat" but most Android users don't have that version yet. It seems to me like GNOME was right on time.
There is nothing to strip out. The GNOME Software app (an app store) has an optional Flatpak plugin but except for that, nothing in GNOME depends on Flatpak.