Sorry, I'm just annoyed at the game outcome tonight and I don't want to think about the injury consequences further. I normally just ignore misguided articles like this...
Yes, I know (or used to know) what Markov chains are and I mislabeled this probability tree as such.
That being said, I think Burke's put more thought into it than you realize (e.g. notice that the TD/FG/punt split in the upper branch is different from those in the lower branch and the root node, reflecting the fact that an offense that is behind in OT will be in 4-down mode).
Burke's refined ESPN model claims a much lower edge for the receiving team, but I like his cruder model better because it's transparent and tweakable.
The best place to start tweaking is at the root node, of course. I did notice is that it leaves out defensive TDs. According to
this site, there were 73, 96 and 92 defensive TDs scored in the NFL over the last three full seasons. Teams get something like 12 meaningful possessions per game on average, so that's about (73+96+92) / (3 * 12 * 32 * 16) = about a 1.4% chance of a defensive TD on any given possession. So that definitely lowers the receiving team's chances.
The probability of a TD on the opening possession definitely seems like something that could be subject to significant fluctuation depending on skill levels; I'd be interested to see if someone can come up with a good estimate of this for yesterday's game.
Of course, we really need to consider two trees (one for the Patriots receiving, one for the Jets receiving). My rough guess so far is that it's possible that the Pats had 50% or less equity receiving the ball, but it's harder for me to imagine that that was less than their equity kicking off to the Jets.