There is one conclusion that I do not agree with. Near the end, the author lists cases where you will outgrow flat files. He then says that "None of these constraints apply to a lot of applications."
One of the constraints is "Multiple processes need to write at the same time." It turns out many early stage products need crons and message queues that execute on a separate worker. These multiple processes often need to write at the same time. You could finagle it so that the main server is the only one writing, but you'd introduce architectural complexity.
So while from the pure scale perspective I agree with the author, if you take a wider perspective, it's best to go with a database. And sqlite is a very sane choice.
If you need scale, cache the most often accessed data in memory and you have the best of both worlds.
My winning combo is sqlite + in-memory cache.