Why not containerise everything? You need libreoffice? No problem, here is a docker or podman container.
Flatpak is basically GUI-optimized containers. It uses the same technology (namespaces) as docker and podman, just with some extra tools to make GUI-related things work properly. That’s why flatpak apps don’t use the system’s gtk version – they’re running in a sandbox with a different rootfs. You can spawn a shell into the sandbox of a specific app with flatpak run --command=sh com.yourapp.YourApp and poke around it if you want to.
If you’re interested in another approach to containerizing GUI applications, also checkout out x11docker. It’s a small independent project maintained by one guy, nothing big like flatpak, but also pretty cool. The name is actually a bit limiting – it supports both docker and podman, and can run wayland apps as well. One of the coolest features, in my opinion, is the ability to run a separate X server inside every sandbox and forward individual windows to the “host” X server. That way you can prevent apps from spying on your keyboard or other apps’ windows.
