The author doesn't make a good case for "The main value of a software company is the mapping of source code and problem space in the developer’s heads" being a universal truth. There are some problem domains and practical development and deployment roadblocks that simply make certain source code more valuable than others. Nowadays it seems people are more willing to throw money at open sourcing solutions so competing firms don't have to roll their own but thats not a hard and fast phenomenon.
I think "software company" can probably hold the weight of the argument, if defined well.
ie., a Bank maybe finds most of its value in that its code runs, etc.
A software company, perhaps, we could define (1) simply as any company where this is true; or if that's cheating, (2) any company where its competitive advantage derives from its software developing over time.
I think the claim of this article is that (1) and (2) refer, aproximately, to the same companies: ie., that software which is changed to adapt to ever changing needs derives that capacity from the "theory of the programmers" and not the code.