Sorry, I should have noticed this before - the penny only just dropped.
rweathers' RTC library (which you're using) defaults to using a library feature (also from rweathers) called SoftI2C that simulates the I2C connection.
This means you can use any pins you like for the I2C connection to the RTC, but you need to update the sketch. Look for the lines in the example which say:
SoftI2C i2c(A4, A5);
And change them to:
SoftI2C i2c(SDA, SCL);
(Or any other pins for that matter.)
The rweathers library used to support hardware i2c as well (less resource intensive, uses the built-in i2c hardware support instead of simulating it in software). However it looks like that support was recently temporarily removed so this library currently only works with SoftI2C. There are other DS3232 RTC libraries that use hardware i2c.
(If you're confused why A4/A5 and SDA/SCL are not the same pins, they are only the same on Arduino Uno & compatibles with atmega328 or atmega168. Different pins on the Mega!)
Sorry for the confusion.