Laminar Research is still ironing out X-Plane 11, removing bugs and improving things. They have released X-Plane 11 Beta 2 which comes with quite a nice number of fixes — including the calibration issue on some custom hardware.
The list of features and fixes is extensive and you can find it here.
One of the fixes has to do with issues with custom controllers (such as the Pro Flight Trainer) which prevented these to be calibrated properly. After some tests, I can confirm this bug was ironed out and the PFT is usable in X-Plane 11 now.
Get the X-Plane 11 Beta 2
You can get the X-Plane 11 Beta 2 here.