FWIW, it's not what I expect. I used Linux and Solaris extensively between 1995-2005 or so and have been a terminal using Mac user since Mac OS X public beta. My expectation is honestly that CLI programs will do whatever the heck they want and I've never heard of .config. I generally expect both configuration files and application data to reside at the root of my home directory, ideally in a subdirectory if there is more than one file.
If I could choose, I'd prefer for application data (files written by the application for its own use) to go in ~/Library/Application Support, because that's where I expect it to go. For configuration that I would edit by hand, I'm not so sure. Probably would prefer the root of my home directory, where I could at least find it easily without looking it up.