In most cases, a transformer will be described as two port rather than 4 port. Analyzing the winding terminals as two port makes sense for RF transformers with differential connection, e.g. a balun. But it's not useful for determining simple parameters like inductance.
As for your calculation, which kind of port parameters do you refer to with "1,1"? Z, S, whatsoever? Also which inductance value are you measuring? Lh, Ls?
I don't think there is a way to measure inductance in CST. You can simulate frequency of the coils and calculate the inductance of the coil using the formula you have given.
the coils shouldn't be 4 ports but only 2 ports. you can connect one edge port between two terminals in the primary coil and one edge port between the two terminals of the secondary coil.
In the title of this thread, CST is mentioned which is a simulation tool.
I agree that reducing the model to a 2-port is the easiest way to evaluate inductance, with Y/Z parameters. For secondary inductance with primary coil open, evaluate Z22.