Ummmm.... I've read elsewhere that the referee was only told that Taker would be losing the day of the show, but that he certainly knew as the match was happening who was winning and who was losing.
Also, that line about "The rule given to all WWE officials, which came into play in this match, is that if a wrestler does not kick out at two, you go ahead with the count as if it were a legitimate pin in a legitimate competition." isn't entirely true. While there have been times in the past when a referee has screwed up a three-count, there's also been moments when the referee has refused to count the third count and pretended that the fallen wrestler's shoulder was up in time even though it clearly wasn't. The Rock/Kurt Angle championship match from No Way Out 2001 sticks out as an example, if I recollect correctly. There was also a moment during the Angle/Michaels match at Wrestlemania 21 where you could argue that Angle didn't get his shoulder up in time after the Sweet Chin Music even though the referee said he did, and there were noticeable boos from some of the audience because of it. These type of scenarios wouldn't happen unless the referee was deliberately ensuring that the wrong person didn't win.