The real question is why do flatpaks exist at all if you can just run programs in containers
flatpaks and containers use the same kernel tech underneath, cgroups and namespaces, it's just a specific implementation designed for desktop apps, and it has things like portals and stuff that's specific for gui apps. So for example, if you use silverblue, you use htop, but it wouldn't make sense as a flatpak when there's a full fedora installation delivered via a container already on your desktop, you'd just dnf install htop and move on.
But not if it takes away my ability to make my system fit my needs.
This is the problem with the term "immutable". For some reason people seem to think that these systems take away configurability and freedom to tinker, which is wrong because the entire point of cloud native is composability. You declare what your system is supposed to look like, and then a deployable artifact comes out the other end, that's pretty much it. Hope this helps!
This is usually an oversight by people who might not have deep linux technical knowledge. I left a polite reply to let them know that AMD is good to go.