Create an empty project using "File" -> "New File or Project..." -> "Other Project" -> "Empty qmake project".
Creator will not populate the project tree, not even with the pro-file itself. In "General Messages" you can read:

Could not find qmake configuration file default.
Error while parsing file C:/Users/rob/dev/src/creator-squish/tests/system/testing/qtcreator_ir4sa-/EmptyQtProj/EmptyQtProj.pro. Giving up.

Even with an empty pro-file, Creator should still show that file in the project tree.

So far I could only reproduce this with the packages from qt.io (Linux, Windows) which are based on Qt 5.4.1. With my local builds based on Qt 5.4.0, I can't reproduce the problem.

Found and tested by Squish test tst_debug_empty_main.