Happy to report that all applicable benefits were granted in a recent ITA itinerary. I put my Skymiles number during booking but the system did not recognize me during booking. Did OLCI and the app/ website were charging me for the seat selection closer to the front.

At the airport the check-in agent entered manually the Skmiles number again and we received:
2 bags each
Free seats anywhere in the Y cabin including front seats and exit row
Fast Track security
SkyPriority boarding
No lounge access due to the itinerary being purely domestic