I didn't want to respond to such a fair question in an overly cavalier fashion so I spent some time going back and talking with the little guy about the matches he played and his perspective on this matchup.
First, let me say that, as my article indicates, we didn't exactly test this list like crazy and we were more concerned about match-ups that were probably better for us than Night March. I remember talking with Shawn C.'s dad during the finals round and he said, "Well, I guess Shawn gets second again!" (Shawn had taken second at VA States the prior year (My son had lost in Top 4 to the eventual champion Davis Norman, now tearing up Seniors)). My response was just because my kid 2-0'd him in Swiss didn't necessarily mean anything - this is a tricky matchup to navigate and it could go either way.
Second, there is no question that a master would view Shawn's list as deficient. He didn't have Target Whistle and I think Liam realized that after the first game so he was just throwing away Mega-Ray's almost recklessly via Battle Compressor, etc.. The result was that we were able to create a game state mid-game where it was just this one Jolteon pounding and pounding with nothing else on the board.
Also, the deck was slower than a typical Night March list might be - fewer Shaymin and not a lot of Acro Bikes, I think, resulting in more time to develop a good board state. There was never a Night March T1 for 180.
There was one game in Swiss where Shawn started to play very slow early - not playing a Sycamore for a turn when he had the chance and Liam realized that he must have a tech Enhanced Hammer that he was not wanting to jettison, but Liam was able to concede prizes while attaching a second Lightning Energy, then when he attached the DCE and the Hammer inevitably came down, Liam had the third Lightning in hand to sweep the game.
Finally, when I talked with my son about the matchup, he thought the Jolteon took it from a 0/100 matchup (We had played Night March at Cities and pwned a Mega-Ray deck, 2-0'ing it in ~5 minutes to win his final City Championship for the year in Chantilly) to a 40/60 matchup. He thought that if the deck had been better designed, while difficult to hit the combos to play around Jolteon, it is still a bad match-up. But if you get to that magic board state, you get there!
I think in the final game, my son used AZ ~4 times to pick up Pokemon in the final few turns to preserve his board state. Go, go Puzzle of Time. The slow development of our opponents Night March definitely held him back in that regard. I would not assume that this was replicable.