OK, an attacker capable to attack the hypervisor when running as root may be often "game over" if it runs as regular user. But that kind of attack is so rare, why is it the base of the argument at all?
Meanwhile your browser/other big SV application/script from Github can become root whenever it wants, or by accident. It can send contents of the whole VM over the Internet to anybody. Or an honest bug in it can destroy your whole VM. This is why the unix privilege separation or even more capable MAC systems exist. Seriously, running untrusted applications with root access is a braindead idea.
Anyway, Qubes team is not against such kinds of isolation: https://qubes-os.discourse.group/t/isolation-within-the-same....
For that to be true, one would have to run each application in a dedicated VM. A great idea, but Qubes does not recommend that for efficiency reasons. It does pose performance and usability challenges which is why most people do not use it that way. So yes, you do care about applications in single VM not snooping/manipulating each other. Luckily there are standard unix and MAC mechanisms to isolate them.
Also, there are disposable VMs for truly untrusted things.
See here for details: https://www.qubes-os.org/doc/vm-sudo/
You can replace passwordless sudo with a secure user prompt: https://www.qubes-os.org/doc/vm-sudo/#replacing-passwordless...