1. Build per-repo build of Qt, including qtquickcontrols2.
2. Set up a kit manually for that build in Creator.
3. Open qtquickcontrols2/CMakeLists.txt and import the build from earlier. The project will be configured using an automatically generated "Imported Kit" instead of the manually defined kit.

The correct behaviour can be seen when importing qmake builds; Creator sees that the build belongs to an existing Qt version and sets up the project using the correct kit.

Comparing the manually defined kit and the generated Imported Kit, the only difference I can see is that the Imported Kit is missing a Qt version.