I've not used the Mega, but since the same notes occurred with the Uno Rev 3,:
1.0 pinout: added SDA and SCL pins that are near to the AREF pin
I can't see anything near the AREF pin labled as SDA or SCL.
Check underneath the board, the 2 pins are labeled down there for the Uno. It should be the 2 pins closest to the USB socket, right next to the AREF.
Would these differ in any way from pins 20 and 21 that are labed as SDA and SCL?
They don't. Just another place to grab them from.
It goes to the USB->Serial chip, which is another Atemga processor (16u2): http://arduino.cc/en/uploads/Main/arduino-mega2560_R3-sch.pdf