Correction to this. MOST appliances do examine and qualify DNS traffic now. This hole was plugged quite a few years back by many vendors, including Fortinet. DNS inspection (Port 53 DPI) is now enabled for most devices by default. These appliances are designed to examine DNS traffic for malformed/mangled/ surreptitious DNS traffic.
It's easy to test. Install a VPN that can use Port 53(DNS) for VPN activity then fire up the VPN. Does the traffic get detected? If yes, then your appliance is detecting Port 53 abuse. If not, then you should check your appliance for DNS bypass exclusions and/or DNS inspection policies. Then add to this, MOST IPS has DNS malformation rules. Including SNORT for PfSense, Untangle, etc. Which usually spots DNS malformation/manipulation (Port 53).
So this is really only a problem for consumers or businesses that cheap out on their security/IT. The first DNS malformation malware we've spotted goes back over a decade, so what's the excuse, right?