@kyle I deleted my reply to this, because I realized it was somewhat ignorance of Flatpak based. I know Flatpak isn't a great solution where storage has higher costs.
I would think that Qubes might still have a storage and security advantage. Thoughts on Qubes vs. Bluefin?
@lwriemen Qubes definitely has a security advantage, because it is using hardware virtualization features to isolate software from each other, and with containers you are relying on software controls enforced by the kernel (if enabled by tools like bubblewrap within the container to begin with, some Flatpaks are pretty locked down, other’s less so).
@lwriemen Space savings is a tougher call. Even if you only have a single VM for everything, you still need that space for that base image. Base images inside flatpaks are likely smaller than a base Qubes Debian/Fedora VM.
If the base VM image doesn’t have the system libraries a particular desktop app needs, and other desktop apps in a different Qube uses some of the same libraries, I would think both of those layers on top of the base VM would have dupe packages in them. So a toss-up there.
@lwriemen At the time apt came about, we did have a way to essentially "vendor" dependencies with software via static linking, but storage was too precious so dynamic libraries were preferred. The hope that containers presents is in no longer having to factor in system software dependencies in your code (dependencies that are often out of date). It comes at some storage cost, but for desktop systems storage isn't nearly at the kind of premium anymore.