In file Engine\Source\Runtime\Engine\Private\PhysicsEngine\ConstraintInstance.cpp
In function FConstraintInstance::SetRefOrientation()
The line
FTransform URefTransform = FTransform(PriAxis1, SecAxis, PriAxis ^ SecAxis, RefPos);
is using PriAxis1 instead of PriAxis.
Current workaround I’m using : Instead of passing axes to SetRefOrientation(), use the axes to create a transform and pass it to SetRefFrame() which ends up passing the correct local pose to the joint.