MM3, it’s not a change of rules, it’s just not well understood. When a wild throw that goes out of play is the first play by an infielder, then the runner is awarded two bases, and the two bases is governed by the position of the runners at the time of the pitch. Since Wainwright was already at 1B at the time of the pitch, he was awarded two bases, moving him to 3B.
A counter to that would be if Wainwright had clearly legged out an infield hit to an infielder who made a bad throw into the stands, then Wainwright would be awarded two bases from where he was at the time of the pitch. So in this case, he would be awarded 2B, which is two bases away from home plate where he was at the time of the pitch. It would not matter if he had already crossed 1B safely before the ball went into the stands.
EDIT: I now see I posted after triple, but we are essentially saying the same thing.
Yeah, that rule is pretty complicated. A lot of umpires get that wrong (not necessarily at the MLB level, but college and below). There was an incident of one of my games once upon a time a thousand years ago and I boned up on my rule book after that.