@raven-worx Yes, your are right that it is a little unclear in the term that I had used, I think the term that actually used for BLE pairing is PASSKEY rather than PIN-CODE, but essentially the question stays the same. I have updated original question accordingly.
Sorry for not answering on that for too long, but at the end of the day I have finished with using Bluez-Qt library. I had to update it with Low Energy functionality by myself, but it was rather easier for me since I am familiar with Bluez DBus Api.
So, AFAIK, the Qt Bluetooth module does not provide any functionality similar to what Bluez's agent provides, i.e. it is not possible to perform general pairing/bonding procedure with different IO (Input-Output) capabilities. Please correct me, if I am wrong.
Ah right - "configure" is ambiguous due to the two step configuration, once by the configure script for qtbase and once by the qmake for the other modules.
This is not so obviously that the summary of the configure script does not warn about disabled features in submodules due to missing dependencies.