In the VE, charging and voltage regulation is controlled by the BCM.
Not sure how it all works within VE but it sounds like a complex system if it's anything like the one in the VF's.
Within VF's, there is a Battery Current Sensor that is used by the BMC to determine net amp hours of usage (state of charge and battery health), both when teh car is in running state and off state. The battery current sensor is a three wire device and considered a servicable component which is connected to the negative terminal at the battery itself.
The VF charging system has lots of smarts build in to the BCS,BCM/Alternator, etc whereas previously in dumber cars it used to be done cheaply and easily with a couple of wires going from the battery to the alternator and its inbuilt regulator. Times change.
If the car was a VF, and since one has already verified the fans and alternator are OK, it could be a either a BMC fault or it could be a Battery Current Sensor fault or a wiring issue between the two components. And as the charging system has lots of smarts based on predefined calculations for a given battery type and size, it could also be a wrong battery is installed (throwing out the predefined calculations used to determine battery status).
So, assuming teh VE is the same as teh VF, the OP could possibly check the correct battery is actually installed and check whether the VE actually has a battery current sensor fault which should reflect as a fault code (?DTC B1516 errors in VF?).
Basically when working on modern cars, service manuals are an absolute necessity, not a luxury.