What pins to use for I2C bus with AVR Mega2560

is the assumption that both pins 20 and 21, as well as SCL and SDA pins near the USB terminal are the same

You don't need to assume anything. You can look at the schematics for the board, or take a magnifying glass and follow the traces on the board. See that pins 20 and 21 and the SCL and SDA pins are connected by traces.

and operate in the same manner

That copper trace between them assures that that will be the case.

and effectively can be used for the same purposes ?

That copper trace between them assures that that will be the case.