The topic and the ensuing discussion is all interesting, and is good content for this board.
It seems logical that if you want to have the maximum amount of energy left with 400 to go, then whatever you can do in the first 1100 to conserve energy while also maintaining strategic position will impact how fast you can go in the last 400. Running extra distance to hit the same pace has to cost incremental energy, no matter how small an amount, leaving a small fraction less available for the kick. This could cost the fractions of a second between placing or not.
In Johnny's case though , here's an outlandish thesis: He had an OFF DAY. He's human- it happens, and for all sorts of reasons. His last 400 was no where near what it has been in other similar races regardless of lanes. 9 times out of 10 he can close in 52, but he just didn't have it that day.
JG is an established great runner , clearly one of USA's top 3-5 on most any day. I will say I see him as a 3:52 miler not withstanding the 3:49 as I think race times on the BU indoor track are an anomaly for most. In the past season there were virtual journeymen no one has heard of who ran 3:54, 55 there that while trying to peak on an outdoor track are a good 3-4 seconds slower.
Maybe someone with the time can look more closely at the disparity between times in and out at BU and offer a plausible explanation.