> The first [base] one being the window’s main content and the last one [elevated] anything above it
This isn't quite true.
1. An iPad app shown in Slide Over or Split View Multitasking will always be elevated (even the main window's view controller).
2. A modally presented view controller with the Full Screen (or Over Full Screen) presentation style will use the same interface level as the presenting view controller. So, on iPhone (or full screen iPad), a full screen presentation will appear above the main window, but still have the base interface level.