Look, you gave the openbsd example, and that's the right way to do it.
Flatpack's are for packaged software-deployment, those are two different things.
Why the need for a sandbox if you could do it much cleaner with things like pledge? But in typical linux fashion, just put another layer on top the pile of garbage so it stop's to stink for a while.
>Well - why would I not want that?
Then please start with the most obvious application sometimes called kernel.
Instead of rigorously integrate something like SElinux they throw layers over layers of half-backed "sandboxes", up to the point to separate applications with Xen (Qube-os), then you find out about Meltdown, and we are back in 1990.