The Sign of the Cross after the penitential rite comes from the old form of the Mass. Quoting the New Liturgical Movement blog quoting another document source]:
This habit came about because in the Tridentine Mass the Indulgentiam prayer, which followed the Penitential Rite, started with the sign of the cross. Back then, many Catholics would cross themselves during the Penitential Rite in anticipation of the Indulgentiam. At Vatican II, the Indulgentiam was removed from the Mass, however, many Catholics still have the habit of improperly crossing themselves during the Penitential Rite – even though the Indulgentiam is gone.