You could define reference angle as: the angle between the two bodies at which other functions will consider the joint angle to be zero. Here 'other functions' refers to any other function of the joint that deals with angles, eg. GetJointAngle, SetLimits.
It's only necessary to have some standard baseline to measure against, like when we say Mt Everest is 8848m high, we implicitly mean it is 8848m higher than sea-level, because sea-level is by long-standing tradition considered to be zero for altitude measurements.
For example, suppose you and I are both standing facing north. The angle between us would be zero, so if you asked anybody what GetJointAngle is for us they would say zero. If I turned to face west, they would say GetJointAngle is now 90. But how about if everybody agreed that when I was facing west, we would call that zero instead... in that case, when I'm facing west they would say zero, and when I'm facing north with you again they would say -90.
Obviously a reference angle of zero is the most intuitive case and I have never found any need to set it to anything else. In fact I feel it could have been left out of the joint def structure altogether.