Unfortunately there are some features on the Arduino IDE that are not available yet, however they are been revised in order to implement them, but there's no ETA on them.
Now, for your specific case there is a workaround, you can use I2C from the Linux console, you can check this link so you can learn how to do it.
OK now I feel a bit foolish.
As stated above, the mini_RTCPro DS3231 works properly with the Arduino Mega 2560 at 5V on Vcc. since it has built in levelers for 3.3v
On a bit of a whim, I changed the Vcc supply from the Edison to the clock to 3.3v instead of the 5v I was using..
Now I can read and write correctly with the same software Sketch attached to the OP.