See screenshot: qt5/qlalr/qlalr.pro and qt5/qt3d/qt3d.pro are loaded and show the src subdirectories, so it's possible to drill down and find source files. In the other projects which are loaded, it's not possible. In older versions of Creator this was working OK. qt5/qtdeclarative/examples/quick/dialogs/systemdialogs/systemdialogs.pro is also loaded; that has all the source files in the same directory, so Creator shows nothing under that branch of the tree.

Toggling "Simplify Tree" does not fix it. Removing .user files before starting Creator (and reconfiguring the shadow build dir again when loading each project) does not fix it.

It seems to work correctly more of the time on OSX, but I'm not sure if it's 100%.