Might be a really stupid question, it's late here, be gentle: but why not just dockerize all applications and let them bring their own libraries etc by default? Wouldn't address similar issues with "everything neat and tidy"?
I don't currently run Silverblue full time but I could see myself doing so in the future.
Regarding docker containerization specifically (or a different OCI-compliant runtime like Podman), it gets very hard because of things like video and sound (Pipewire should help immensely), but also there are lots of apps that you want to have uncontainered access. Like Vim becomes a lot less useful to me if it's filesystem is contained.
Having a full Gnome install on every app, a full KDE install on every app. Having to install a given theme into every single docker container.
Maybe I'm missing something. I'm not even sure how this could make sense.