Had similar concerns about the default sandboxing, so had to use `--sandbox` with every app and then carefully engineer the permissions so the apps would actually work.

After reading about potential future problems with Flatpak on my distro, I decided to experiment more with Bubblewrap. It turned out to be surprisingly easy to build a minimal container manager around it (here comes the shameless self-plug): https://github.com/pakstak/pakstak

Although for desktop apps, it is not as easy as just packing an app into an OCI container and expecting it to work. Since you are basically building on top of the kernel, which brings true portability between distros, you have to provide the userspace part of the drivers, and this layer depends on your hardware. Overlaying an app container on top of a "driver container" can help with this though.