I am not sure I understand the question. The S-parameters are stored as 3D matrices, with the last index spanning the frequency. An N-port at F frequencies will have the size [N N F], that is NxNxF, where N=2 for this 2-port case.
I'm finding an issue with SXPWrite.
It does not support or properly truncate scientific notation- a number like -9.8235e-5 ends up being written to the file like -9.8235. This is a HUGE problem! Otherwise a great set of tools.