As far as the refs go the controversy is not whether anyone could see if JT made a TD or how far forward he went but they could easily see that he went as far forward as he could and then was getting pushed and dragged back 3-4 yards but still had the ball when this is occurring. Hence, you blow the play dead and call forward progress. Even if you see Swann start to rip at and get the ball loose at the 4 yard line and haven't yet blown the whistle that should make the ref blow the whistle at that, already late, point in time. It would then have been like a zillion other plays where a defensive player is ripping the ball out while "playing to the whistle" and then tries to run with it but everyone else knows the play was dead and the refs rule that it was dead.
I will always think, however, that it should have been Byerly running it if you are just gonna call a QB draw or sneak up the gut on the goal line. No reason to suddenly change after a number of games of consistently using Byerly successfully in that situation. If you keep JT in then let an AB lead block for Days and have him power it in the middle or run the fleet-footed QB to the edge and the pylon, that is, play to JT's strengths.