Would you say that a database is a "black box full of binary garbage, chewing gum and rubber bands that tightly couples everything in Windows.and it's like spaghetti and can't possibly be unwound"?

I don't think you would, that's not the conventional wisdom. Databases are considered to be the epitomy of clean, reliable, and efficient representations of data. It is text files that lack these capabilities and are considered a non-standard mess when it comes to data.

The registry is just a database. It may have not seen the best usage it could have from windows and applications, does that make it a bad architectural decision? Would we think different on the registry if it was just SQLite (or would we in this case think differently of SQLite)? Personally I firmly believe that the registry approach is a great architectural decision, for all the reasons outlined here: https://sqlite.org/appfileformat.html