I think the reason people use text file + "snowflake software" is that they want just the structure (constraints) they want, and no more. BTW, what people want changes over time and by circumstance.

org mode has a lot of features, including customizability, but imposes some heavy constraints as well. By its nature it's only going to satisfy a sliver of the people who have come around to text file.

It's good you linked that document, though. At a glance it gives a fair idea of what you'd be buying in to.