This argument used to be used all the time by WiFi device manufacturers, and it turns out to be bullshit. The truth is that you, the operator of the device, assume all liability for your modifications, but there is no reason you can't flash/modify your firmware to, say, improve your power-saving abilities or improve your scanning times.

We have enough source code for Atheros devices to be able to reprogram them as we see fit, and the FCC doesn't really care.