The Lionel Corporation removed the port-holes in the PW era. They also removed the nose-grabs, two piece cab ladders, and the screened vents. These were all gone by the time General Mills got a hold of the dies.
Once General Mills began production, the first F-3's were essentially copies of the late Lionel Corp F-3's, lacking port holes, screened vents, nose grabs, two-piece cab ladders, plus the elimination of the nose vents.
Over time MPC removed the side vents as needed to allow for fancier decoration, along with the addition of the much-loathed ridges along the bottom edge of the die which helped in the printing og the stripes on the Santa Fe F-3.
By the late 70's the trend began a slow reversal, first bringing back the ports and nose grabs, then the two-piece ladders, then the screened vents, then the nose vents, then the side vents, and finally the elimination of the bottom ridges.
Jon 
