Since the introduction of qtchooser /usr/bin/qmake is not the correct way to detect the Qt Kit available, because this is actually qtchooser masquerading multiple versions.

I think th eocrrect approach would be to call qtchooser -l (or --list) and for every version that outputs run qmake.

For example, if qtchooser -l outputs:

4
5
myown5

Then three kits are available, and qmake should be called three times like:

qmake -qt4
qmake -qt5
qmake -qtmyown5

(note that you can also use qmake -qt=myown5)

Even more, due to the nature of masquerading things of qtchooser, this might be needed to be run every time qt creator starts.

Note: this bug may seem similar to QTCREATORBUG-9841 or QTCREATORBUG-9068, but I think the root problem is different.