I'm running an immutable distro at the moment (GNOME OS), and I felt no loss of performance due to Flatpaks. Snaps, on the other hand, do have a perceivably longer launch time.
Given that it's an immutable distro, everything I need needs to be either a Flatpak, a Snap, an Appimage or an extracted tarball, otherwise it runs in a container. The advantage of this system is stability and making the host incorruptible, as well as the ability to very easily roll back updates or failed systemd-sysext layers.
Not everything can run in a Flatpak at the moment, but we're hoping the evolution in Flatpak, XDG portals as well as encouraging developers to use the available XDG portals can make this a possibility someday. Namely, IDEs don't run that well in a Flatpak, but GNOME Builder has proven that it's 100% possible with the currently available XDG portals as well as connecting your IDE or editor to a container.