He claims they were expensive, but in the top of the article he states two other things: That it's been so long he can't be relied on for accurate recollections, and also that when they first started using door, it did in fact make financial sense.

Most doors have a margin that can be cut to the desired height, which is what "tfa" said was done. That doesn't make it a custom door though. The author said he observed the desks being made, so it sounds like he saw them being cut to the desired height and, not knowing that was common for doors, assumed they must be expensive and therefore custom.

Maybe they were expensive! But the author is not a reliable narrator on the topic, and without some better evidence I'm not inclined to believe amazon went from using typical solid-core doors for a while, but then went out of their way to find very expensive doors.