Okay, I've got no way of testing this, as all runways near me are almost at sea-level. I always thought that setting the QNH would fix altitute readouts correctly. So, check that:
1. You've got autoset QNH ticked, and the correct airport setup, on Smartview, and the QNH pressure is correctly set.
In my screenshot, I have EGQK (Kinloss) selected as the airport, and that is currently reporting a QNH of 1017.
2. You've set the transition altitude in preference. I have mine set to 9999, so that anything below 10,000 feet (FL100) is corrected for the airport QNH.
See screenshots attached.