miniPCI cards don't have the ports on them, they are just modules. Sometimes, you can add/remove ports depending on the module you're adding, but in Gateway's case, they simply added all of the ports to simplify manufacturing.
According to the specs I've seen, when the HPNA module is installed, the modem ports are using for HPNA (eeffectively disabling the modem) and the Ethernet port is simply dead. When the Ethernet module is installed, the modem ports are used for the modem, and the Ethernet port is used for ... Ethernet. :)
I ordered my GCT with the Ethernet module, so I should know in a few days.