The first thing to keep in mind is that Xml configuration is not the only way to achieve any of your goals here.
The Xml configuration was extremely error prone, especially compared to the strongly typed registration DSL or using type scanning registrations (what most users lean on now) and caused me a *lot* of work in user support.
"I also have a separate Container project that references the interfaces project and the concrete type projects." -- Okay. I personally don't think that this kind of assembly reference is actually a problem, but if you still insist on it you can have StructureMap discover Registry classes in assemblies scanned from the file system. That's how users are handling that today. It's more complexity and very easily confusing for new devs, but you've got the ability to do that.