Assuming you have a non-refundable coach fare, then you would only have to pay the fare difference, even if it is only $0.01 higher. As long as you are transitting, it is ok.

The rule for UA operating SYD-MEL-SYD is that ONLY online international connections are allowed. Sometimes agents goof and that may not be the case, but that is the rule. You are fine in this case though.