As you said, passer rating takes into account all of the above stats, except for 1 lost fumble and 2 rushing TD. The large delta of 11 shrinks down to a difference of 3.
And although Rodgers did have more TD, that was only as a result of having more attempts. Romo's TD% was higher. Rodgers had an excellent INT%, which is typical for him. As I believe you have mentioned before (correctly), Rodgers is extremely cautious, and will take a sack or throwaway more often than he will take a risk, especially late in games. This is part of why Romo usually has more comebacks, game-winning drives, and much better late-and-close numbers. This season was no different.
2014 in Late and Close Situations (4th qtr or OT, + or - 8 points)
Romo 114.6
Rodgers 84.4
But make a good case with the full-season TD/INT ratio. Obviously, since Romo's full-season rating is higher than Rodgers,' there is much more to passing than TD/INT ratio, but these are probably things that aren't as easy for the voters to get a handle on. Romo led the league in both yards per attempt and completion percentage this year, which had only happened in 8 of the last 37 seasons. 6 of the 8 QB who did it won the MVP award. That doesn't mean Romo will, of course. With only one point separating them in pass rating, history says the "tie" will almost certainly go to the bigger name, and the better player.