To be fair, Microsoft doesn't rely on the registry for complex configurations either, even IIS uses .config files.
Its only really big misstep (apart from the fundamental issues with the registry in general) is that file associations and COM registrations are all intermingled in the same namespace. But those can be and are interconnected (see how the Office file types handle their registrations, for example), so it's kind of understandable how they ended up where they did.
Except that is for serving from a single file share ir a replicated site across a farm of IISes.
This has nothing with 'complex configurations'