Are you seriously acting like every application having full access over other applications is not an actual security issue?
See my other comment too.
There is a lot more to desktop inter-app security than “if an app had a root shell then it could compromise things”. A great many attack vectors that we see constantly have a much narrower ingress than that.
Virtualization is another thing entirely. But if you want it that way, then why not simply start a second X for the untrusted app?