Everybody who had access to this format can take it over. It can do far too much, that's why everybody uses JSON. It can only represent hashes, arrays, and some limited primitives. No links, no logic, no lib. But lua is far too powerful. Game over.
Lisp would be even better, btw. Much easier to parse, and much easier to avoid eval. But his idea is eval.
The author doesn't mention it explicitly, but I think that's his case.
For his situation, I think it's a good use of the tool.
Lua is not far too powerful, Lua is as powerful as you want it to be.
In what format, that you then have to parse?
More powerful features can also be helpful if you have a large config file that would typically need to be generated by a separate program. One example of this is shown in the linked blog post, when they use a for loop to initialize a large array that has many similar objects.
It can also help if the config file starts gaining special "PRAGMA" fields over the years. There is a certain tendency for configuration files to slowly evolve into an ad-hoc and poorly implemented scripting language and in those cases, switching to a proper programming language cuts the problem at the root.
That said, for data exchange situations JSON has the advantage that it is more well-behaved in the case of malicious inputs.