The key part of this that differentiates the two, is the part I've highlighted.Well this is straight outta wiki...
"A rootkit is software that enables continued privileged access to a computer while actively hiding its presence from administrators by subverting standard operating system functionality or other applications."
No security software will stop everything, nor should it be relied upon to stop everything, which is why most in the sec com, recommend a layered approach.I have seen viruses disable these things and still display the av is running fine. Mostly I have seen these specialty viruses in office servers collecting data.
So I say that running it is just a waste in resources as I have to scan with a rookit remover all the time anyway.
Just because something gets past the security software, doesn't mean you should just remove the security software. Either replace the security software with something that has better detection/protection, or report the missed infection to the security softwares vendors, so action can be taken to prevent further breaches.