I use Scrivener on both my PC and my Mac. I share files via Google Drive. When I create a new folder on my PC by clicking on an existing populated folder in my binder, the new folder opens already populated with content from my Mac folders. When I create a new folder from a blank, untitled folder, it creates a new, empty folder as desired.
Just to make sure I understand, by way of example you have a folder in your binder called “Apple”, say, and in that folder there are three files, “Fuji”, “Honeycrisp”, and “Washington Delicious”. So you click on “Apple” and make a new folder by using the Project/New Folder menu command. This is in fact makes a sibling folder, not a folder within Apple, but I’m assuming that’s what you mean. This folder comes up, and it already has the three apple files in it. However if you click on another folder, “Oranges” that has no files in it and create a new folder, you get an empty sibling below it?
Second question, you mentioned sharing files via Google Drive, does that mean you have placed your .scriv project folder/package in the Google Drive and are opening it from there on each computer respectively? If so, I don’t understand what you mean by distinguishing something as being populated with “content from my Mac folders”. If the .scriv project is on the Google Drive, then both computers are using the same exact project. There isn’t a Mac version vs. a PC version.