It is really that simple, if the AP has a MAC filter, any device which attempts to authenticate that doesn't have a MAC address on the list will just be denied.
However the problem from a security perspective (which is why this should not be used as a security function) is that it is trivial to spoof a valid MAC address (by sniffing them wirelessly and waiting until the valid user has gone - this is a common technique for avoiding usage costs in airports)
Update to show where MAC address denial happens:
Client --------------Probe-------------> AP
AP -------Probe Response----------> Client
Client ---802.11 Auth Request-----> AP
MAC authentication happens in here. If the client MAC is not on the list the following responses will not get sent:
AP ------802.11 Auth Response---> Client
Client --802.11 Assoc Request----> AP
AP -----802.11 Assoc Respons----> Client
Which is then followed by EAP etc.