Typically an overcharging isolated field alternator is getting 12v to one field terminal and a full ground to the other.
The isolated field voltage regulator provides a variable ground to the field wire.
It requires a GOOD 12V voltage source or it will assume that the alternator needs to output more.
Think of it this way...
If the VR only sees 11v it will try to increase the alternator output to get it up to 12v (nominal voltage numbers for illustration only)
So the alternator might output 15v to meet the load / voltage requirements.
Say the VR sees 10v, same process,
But now the alternator outputs 18v
With the battery in the trunk if the wires feeding the VR are not of sufficient size to carry the load there will be a voltage drop. This drop could cause the over charging.
Measuring voltage with no load gives incorrect readings.