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.