So, horribly unreadable xml config files?

Like S-expressions don't exist. Or even goddamn JSON. Come on, we don't have to jump from one stupidity (unstructured text) to another (using XML as a data representation format).

CSON or .desktop / .service or something similar is immediately understandable to most people and doesn't waste time with unnecessary tokens like XML does.

Not necessarily. JSON is not bad, _if_ you allow comments. Even plain-jane key/value config files can be sanity-checked. I suspect part of the problem is that anything fancy like that is awkward to do in C, so people take the lazy way out.

Maybe many tiny sqlite databases? Then you would not need to to centralize your data in a single database, but still do queries across different config files.

SQLite is a huge win. All the power of SQL, and you don't have to introduce system-wide and non-local dependencies.

How is this a win? Instead of opening a text file we have to write update statements to change any setting. Sql is itself a verbose language that should have been discarded in the 80's.