The big problem that myself and many others have with Andy is that he is a professional. He is known in web standards and design circles. He builds web sites.
The big point here: He has been on the other side of the design process (I presume) explaining to people why things were built the way they were.
In Andy's "redux" he seems to forget this. Blatantly. Thats not to say he isn't right on some obvious things (the Times left-navigation on the Homepage) but for almost everything else he was pretty damn disparaging and ignorant of the process that churns out the end result. To a shocking level IMHO.
What Khoi is saying here is a very level-headed and polite response to Andys redesign. (BTW Andy himself says it wasn't so much a redesign, more like "I examined pressing issues for digital news").
If it had been a graduate who did the "redux" I would have smiled and said, "Come back in a few years working in the real world and you'll see things differently". So I was a little shocked that this came from someone like Andy.
Background Info: Khoi joined the Times in late 2005 or so. At that time the redesign for the NYT was well underway so he was not responsible for the look-and-feel that emerged. For the most part he has been trying to improve on the legacy he inherited - the Sectionfront and Article layouts, the Navigation bars on the Homepage - not Khoi's idea and he fought to change that (take a look at the Opinion section for example http://www.nytimes.com/opinion for one single sample of his stewardship).