Define a schema for any bespoke configuration, it's not too hard. It's needed to make it translatable, but Drupal 8 will also validate your config against it so it's still handy on non-translatable sites.
This post is the first in a series about getting Drupal to run as a persistent server, responding to requests without bootstrapping each and every time.
This is how many other application frameworks and languages run: nodejs, Rails etc.