Does the Arduino Mega 2560 have 2 TWI inputs (just like the Arduino Due, which has SDA1/SCL1 and SDA/SCL)?
So are we able to connect two separate sensors/devices which use SDA/SCL? One to the first SDA/SCL(next to AREF port) and 1 to SDA 20/SCL 21?
No, just one.
Different boards have I2C (TWI, SDA SCL) on different pins, which makes it impossible for a shield to connect easy to I2C. By adding those two pins next to AREF, a shield can use those for I2C.
On the Mega board, pin 20 and 21 are connected to those two next to AREF, they are the same.