I'm not able to build Qt in "commercial" mode from Git. For some reason, the '.qt-license' file is not detected by my configure script. This problem is limited to Git, and does not occur when building from qt-everywhere-enterprise-src-5.6.0.zip.

Is this an intended limitation?

If yes, then http://doc.qt.io/qt-5/windows-building.html (and possibly other wiki pages) should be updated to document this limitation. Alternatively, the issue should be fixed.