You are correct that Ldiff and Rdiff are EXACT if the inductor feed is symmetric. In your case, it is not exact but by far the best method to extract these values. The inductance2 and resistance2 values are NOT applicable for your case.
Regarding inductors with more than 2 ports: Sonnet provides another set of equations for center tapped inductors. For my own general inductors cases, I wire up everything at schematic level and then extract values for the impedance between terminals (=differential values as discussed above).