It's kind of like the general distaste for setuid binaries. If you have a correctly-written setuid binary, then you can use it to sandbox a process by, say, running it in a chroot. But if it's not correctly written, you have problems on your hands that far outweigh the problem you were originally trying to solve. So a random desktop app that ships with a setuid helper binary is going to be seen with suspicion. (Chrome is the only one I can think of that ships one, but they probably employ the people most qualified to write a bug-free setuid app, and they're getting rid of it in favor of user namespaces anyway.)
Of course, for the average developer desktop, processes probably have fifteen ways to gain passwordless root anyway. I certainly set sudo to nopasswd for convenience. :) So on a developer desktop, it's a nifty hack, although it doesn't gain you security against a malicious app/exploit. But as a general-purpose sandboxing approach, it's a bad tradeoff to make.
This stuff is only sort-of reliable when-containers-dont-have-root-bug-today if you run that as a separate user than yourself in a different X server
So basically not cool.
The way GNOME is doing ACTUAL sandboxing is much neater. Turns out it doesn't use Docker also. Go figure /sarcasm.
So your "when-containers-dont-have-root-bug-today" applies to Gnome too...
Also: there is no such thing as 'actual' sandboxing. There are many forms of sandboxing, containers (not docker-exclusive, as Gnome is using it exactly the same way) is one form, but we also know Virtual Machines, the Java VM, Javascript in a browser, ... the list goes on - all meaning the same thing: shield an application from everything else on the computer and try to prevent it from breaking out.
Of course, there have been other vulnerabilities in the past allowing containers to get root. And the X11 weakness alone is enough to not treat this as a security layer.