In the case of not using a VCS system "sub-optimal" means he's making his own life difficult for no gain. It is difficult to see that it is anything other than a mistake - a 20 year old project with 700k lines of code is going to benefit from version control. The only saving grace is that Dwarf Fortress development predates git so at least there is a good excuse for how it happened this way, but it is still a mistake.
We all make mistakes though, so the world will continue to turn if Tarn sticks to it.