Well I succeeded to calibrate the E1200 Pro motors - however I needed to apply a trick:
Since you can start calibration in QGC only when no battery is connected and the FC will immediatly send the calibration signal as soon as it is powered via the ACSP4 you have to do the following:
1.) Disconnect the ACSP4 from Pixhawk
2.) Power the Pixracer via USB
3.) Connect LiPo to ACSP4 (ESCs will slowly fire up and get ready)
4.) Connect via QGC and start ESC calibration (it will let you do so since no battery is deteced)
5.) When asked by QGC to connect the LiPo now, replug the ACSP4 to Pixracer
6.) Pixracer will think the battery has just been connected and send the calibartion Signal to the ESCs which are already "booted" and Ready.
Viola - Done!
However this could be much simpler if the FC would allow the ESCs to become ready once the battery is connected.
This can be achived e.g. by adding a delay between powerup and sending of the calib-signal.