For item 3, the warning is that the state-space fit to the s-parameters is non-passive and not the s-parameters themselves. Yes, to address this I would recommend turning on Passivity Eforcement with the "IFPV" option if the model contains just signal nets. Or use "IFPVLF" if power/ground planes are also included. To get to this, right mouse click on NPort component in the Circuit schematic, select Edit model, and then click on the Options tab in that form.
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