There's a page on the Arch Wiki (https://wiki.archlinux.org/index.php/XDG_Base_Directory) outlining how to achieve a pretty clean home dir. I have a pretty clean setup, mostly everything lives in ~/local/[bin|cache|data|cfg|pkg|src|run]/, which are set by XDG_CONFIG stuff. Mostly I source it in my shell profile, leaving one dot (.zshenv) and the compulsory ones like .ssh/ which will never go away. (That's basically to say, it's possible to sort out dotfiles on Linux, I've done it.)

I've taken to using mostly the ndb file format from plan9 for configurations in programs I've written, which have a very nice feature for includes. Mostly I've been well served by them, The example shown at http://man.cat-v.org/9front/6/ndb accomplishes relatively the same as what you've accomplished here, so I can state that your approach would likely be really nice to use, and definitely it's more query-friendly to have something that is predictable for each program, rather than a bespoke offering for every fucking thing. But, yeah. xkcd standards.