I have a hard time believing that'd be cheaper than having a stock of ikea desks and having your new employees put them together on their first day.
Source: Someone that had to put an ikea desk together on his first day at his internship. xD
Honestly that was not the worst place I worked at either.
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.
I guess this a difference between being frugal (or appearing that way) and being cheap. I can tell you from my paycheck, Amazon's not cheap.