The reasoning is simple: if no random third parties ever get full control of your machine, than most likely the OS is going to stay intact (with the exception of possible local privilege escalation exploits).

If the OS is intact, the job of checking whether a user environment is compromised is easy and actually doable (as opposed to the case of trying to find malware on a compromised OS).

If, in addition, a user account has limited privileges (which it should of course), then even when compromised the chances of malware being able to do a lot are a lot less. For instance, turning off a webcam light being a root is probably easy, otherwise probably not. Setting up a server, listening for incoming connections and punching a hole in local firewall as root is available, but as a regular user is not.

Stop giving admin rights to your computer to random people (install software as an admin) and live much happier. As an additional benefit, there's never a situation 'I installed this and now computer is messed up, because Joe-the-dev ran "rm -f " with a wrong path as a parameter'.

I don't agree at all: I think that apps should be installed as admin and auto-updated. I don't follow any of your arguments that installing things as non-admin are more secure.

It's more secure because you don't have to delegate admin access to random people to install the software. Any of these "RAT kits", I guarantee you, requires admin access to the system at one point or another, be it during the install, by explicitly asking for admin password, or implicitly by using the fact that most users are logged in as admin.