While in the registry it's like 5 layers deep and you need to figure out the vendor name along the way.
Also, regedit supports Ctrl+F.
Sometimes it's /etc/$subdirectory/$toolname, doing that very many-layers-deep thing that you describe.
Sometimes, particularly on the BSDs, it's /usr/local/etc.
Sometimes it's ~/.config/$subdirectory/$subdirectory/$thing . Or, if you are lucky, it follows the XDG rules for locating the ~/.config part.
Sometimes it's ~/.$toolname .
The irony is that all of the arguments about where the files are fall apart and miss the point, as the Windows registry hive file system is far more standardized than Linux-based operating systems and the BSDs are.
The real discussion point is whether a structured hierarchical database of key-value pairs with typed values, accessed through an operating system API, is better as an actual database file format, with all that that implies for things like indexing and the elimination of quoting rules, text parsing, and escaping; or as text files just like it used to be with the old loads-of-.INI files system of DOS-Windows 3.