I purchased a DS3231 time clock and temp sensor for my Mega 2560, the 4 pins needed to operate it as I intend line up on the Mega board except the power pin lines up with the AREF on the Mega. GND to GND, SCL to SCL, and SDA to SDA, but then the 5 volt pin on the DS3231 lines up with the AREF. I am wanting to pulg the DS3231 directly into the Mega without the use of a breadboard or jumper wires.
AREF is not a power supply. It is the reference voltage for the A/D converter. You are going to have to connect the DS3231 to something other than that, which will require a jumper wire.
One thing you could try (if you wish and if you're careful and at your own risk), is to bend the DS3231's Vcc pin up and then it would be easy to stick a female-male jumper wire from there to 5V.
The fact that it almost lines up is just a coincidence. Just wire it normally.