In my setup, I installed a CA Certificate on the controller for securewireless.ourdomain.edu and another CA certificate, our domain wildcard cert, on Clearpass Guest.
On Clearpass, I refer to the controller by IP Address as you described. During the redirect back to the controller after authentication, it calls the domainname that my certificate is registered for, securewireless.ourdomain.edu.
I have had no issues with certificate errors on any device, IOS included, save for one small one that I am about to open a TAC ticket for. On an iPhone4s and an iPad 3 running IOS 6.0.1 specifically, using the Chrome Browser only, i get an error that states roughly "This sites certificate reports as securewireless.ourdomain.edu but is reporting its actual name as securelogin.arubanetworks.com do you wish to proceed?" Once they login, the redirect then fails, however, they are actually authenticated and can go on to anywhere.
That is the only issues I have had so far and they seem isolated to the Chrome Browser on spectific devices with iOS 6.0.1 in our environment. All other browsers I have tested on the various OS's seem to work without problems when the IP is referenced on Clearpass and the CA Cert is referred to as something else on the controller.
Anyone else seen these issues?