👋 right on! I actually also have used containers as a key to my security layout before, but yeah you miss out on all the benefits of portage.
I was doing something crazy and actually running Gentoo inside each one! It was very difficult to stay up-to-date. But I basically had my host as barebones as possible and used LibVirt containers for everything, attempting to make a few templates that I could keep updated and base other VMs on. I was able to keep this up for about two years then I had to relax (was my main PC). But it was really secure, and it does work.
The benefit of encapsulation is that you have a lot of freedom inside each container, like install a different distro if you need to. Also as long as they are isolated you don’t need to worry as much about their individual security. But it’s still good to. I ran SELinux on the host and non-SELinux (but hardened) in the guests.
SELinux has a lot of advantages over users/groups, but I think the latter can be just as secure if you know what you’re doing. For example with SELinux you can prevent certain applications from accessing the network, or restrict access to certain ports, etc. It’s also useful for desktop environments where a lot of GUI apps run under one user- e.g. neither my main user nor any other program can access my keepassxc directory, only the keepassxc process (and root) can (even though the application is running under my main user). You can also restrict root quite a bit, especially if you compile in the option to prevent disabling SELinux at boot (I need to recompile my kernel to disable it).
But again while it is fun to learn, it is quite a pain and I’ve relaxed the setup on my new computer to use a different user for everything (including gui apps), which I think is secure enough for me. But this style relies on my ability to adhere to it, whereas with SELinux you can set it up to where you’re forced to