Pickle isn't really a WordPress theme. It's a full-on solution for running a restaurant. It's a platform. I don't see any conflict between it and the "standards" that we normally preach. Users of Pickle wouldn't be switching themes in the traditional sense. Doing so would be like switching from Magento to WP + WooCommerce for your online shop.

Jason also isn't promoting it as a theme. I think it'd be wrong to call it such.

If I had coded it, I probably would've started from the plugins folder in my dev install rather than the themes folder. I think there are a few advantages of doing this, but they probably don't matter since I didn't build it.