I've used JSON as an additional options input to a native-compiled CLI program's various commands because 1) the schema of each option is radically different, 2) they need to be passed most of the way down the call stack easily for each stage of our calculation and report generation.

It works fantastically well, and don't let anyone tell you that you MUST bloat the CLI interface of your program with every possible dial or lever it contains. We should all be cogent of the fact that, in this very young and rapidly evolving profession, textbook and real-world best practice often do not overlap, and are converging and diverging all the time.