The common mode filter is symmetrical in itself. The pin assignment with + and - is primarily there to have the assignment to the same pin on the connector and on the IC.
As long as you make sure that the correct filter is used (D1 for port 1, D2 for port 2) and DN and DP end up "through the inductance" at the correct pin of the IC, everything is OK.
Does it answer your question?
Regards
/Peter
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