I'm not entirely sure I go along with that explanation.
The computer should always know how much gas it started the race with, how much has been burned, and therefore how much it has left. Same story for the distance. It knows what lap it's on down to the corner. From this it should be able to continuously calculate the bike's previous MPG, and the MPG required to make it to the line. It also knows the limit of how much it can lean out the mix. From this data, it should have little difficulty calculating a critical fuel level for each lap. If the remaining fuel falls below this minimum curve, the rider may/will run out gas. The computer will then do what it must to avoid falling 'behind the curve.' It's fairly easy for the software to simply say 'No' when the rider demands more throttle than can be sustained. It can also cut fuel by using a little TC-like injector shutdown on the straights.
I think we've seen this before. Remember a few years back at Laguna, when Pedrosa nearly lost a position to Flossi? The computer strangled his bike and he lost multiple seconds over the last few laps.
I think T3 mis-measured the fuel or did a finger-slip when plugging the numbers into the computer; either would make the ECU think it had more than was actually in the tank. Cal was running gung-ho right till the point his bike stopped. I think the ECU was just as surprised as he!
Maybe the T3 fuel dude was sick and Yamaha loaned them the guy from Ben's team.