If you configure correctly the L3 Rogue detection
This is what it will happen
The Controller will see that Mac address of that AP through the wired and he will see the BSSID(which is the mac address of the AP in the air) he will match it and he will conclude well this is a rogue AP as im looking it on the air and also im looking it through the wired....
Besides that he has other methods to conclude this... you can see all of them in the Rogue AP guide i gave you in the other tread... it is a really useful document...
Anyways if i understood correctly your question which is how the controller classifed that ap as rogue well Collin already explained you when you got the ap classification unchecked you saying ALL The aps he see they are all rogues... and like Collin said it is a very specific scenario in which you will uncheck that box...
If this answer the asnwer of Cjoseph asnwer your quesiton you should use the accept as solution button on the answer that answered it.... :)