I understand, it is not a bad thing at all. It is just that there is no "one size fits all" argument for this - some people prefer having these files outside the theme and some people prefer having them inside. Ideally a theme should support both, though unfortunately in my case I have been unable to support the latter scenario, but not for the lack of trying.
Regarding Atahualpa, I thought you knew!
It is way ahead in the list of popular themes in WP. it is probably the most downloaded free theme ever with over 300,000 downloads. Suffusion has just garnered about 5% of Atahualpa's downloads. Note, though, that the number of downloads is no true measure of a theme's popularity, since there are several good themes that don't get downloaded enough. Hybrid comes across as one such theme.
Different themes operate on different paradigms. Atahualpa's focus is on building out a lot of customization options, while framework-based themes like Hybrid build a lot of features and ask the users to extend them by writing their own "child" themes. My goal was to build a blend of both, so I allow a good bit of customization on the look and feel side, and I also have options to turn other features on and off. I still have some distance to go, though I believe I am catching up fast.