zsellera covered the mechanism of transmission very well. The 125MHz frequency is specifically coming from the Ethernet standard, as its essentially the operating frequency of each pair in typical hundred megabit and gigabit Ethernet. 10Mbps Ethernet operates at 10MHz.

By flipping the port speed between 100 and 10Mbps they are essentially toggling the 125MHz oscillator. I don't think anything is intentially generating the frequency of the tone you hear, it's just intermodulation products of the noise and the LO in the receiver.