I seem to have found a BUG in XCode 9, however I can't submit it, so I'll submit it here and hope one of you that can submit bugs can forward it to Apple.
It's an easy bug to test: Create a project, then create a Group. In Xcode 8.3.3 this would create a Group in Xcode but not a subdirectory in Finder. NOW it also generates a Subdirectory (check your finder directory).
I discovered this by following some directions in a book on Core Data. I started in Xcode and created the groups as described in the book. Later I downloaded Xcode 9 and started over (creating a new project), creating the group now creates a subdirectory also.
This might actually be NICE....if it weren't for the fact that some files, like info.plist are expected to be in the main project directory, or at least it errored when I moved the info.list to the Group, as described in the book (it works in Xcode 8.3.3, does not work in Xcode 9 beta 5).
I tried this in iOS, as well as in macOS (both create subdirectories now). I didn't try the other tvOS or watchOS since I don't use those now.
Let me know if this is supposed to be a NEW UNDOCUMENTED FEATURE of Xcode 9. There might be lots of people who will have to scramble if this is true though.
I note that if I generate the groups in XCode 8.3.3, I can use XCode 9.0 to use them in the previous expected functionality. It's only when you CREATE the Groups in XCode 9 that this anomaly appears.