I am referring to their positions in these threads, especially the comments of Gian-Carlo Pascutto (Mozilla):
That's not really what it says there. Some of their statements about both Chromium and Firefox are also incorrect. They're clearing aiming to promote Firefox and aren't doing so honestly.
On the Flatpak version, it is different. Flatpak itself uses namespaces, chroots and secomp-bpf-filter for its own lax sandbox, which encompasses the app as a whole. It uses a secomp-bpf-filter for generic container types on Linux which blocks namespace and chroot creation inside of a flatpak app, because these syscalls would otherwise lead to easy escapes of flatpak's own generic sandbox. But since these syscalls are blocked, FF also can only use secomp-bpf-filters for its own processes and not chroots and namespaces anymore to confine its processes as it does on the non-flatpak version. So the namespaces and chroots around each process got replaced by a more generic flatpak sandbox encompassing the whole app. This leads to a less tailored and thus weaker sandboxing architecture, which neither protects sites, nor stored browser data, nor the system as a whole better than the native version.
Firefox doesn't have complete site isolation in any form, whether or not Flatpak is involved. It's also a weaker sandbox. Flatpak weakens it further. You're mixing up several different things.