1. Create a new project, e.g. "Qt Console Applicaton"
2. Build the project
3. Go to Projects mode / Build settings and notice the "An incompatible build exists in ..., which will be overridden" warning.
4. Build the project again, warning still exists.

The kit is configured with an installed Qt 5.4.0.

As the consequence building an application always calls qmake, which can take a while for bigger projects like qtcreator.pro.