X2 on testing the whole system, as opposed to individual parts when you've got a head scratcher of an issue.
As I was reading through, I was going to recommend checking the "pigtail" connector & it's wiring as well, because this area USUALLY causes the type of problem you are seeing. It's the communication between the alternator and the ECU, and MUCH more likely an issue than the ECU itself.
The OTHER odd thing seen B4 here was an alternator that passed a quick test, but STILL had a bad diode, NOT too common....
P.S. - an easy check to see what's going on with intermittent voltage issues, is to use a cigarette lighter plug to hook a voltmeter to so you can get a reading when the light comes on - sometimes easier than always driving around after setting the car to diagnostic mode so you can see it on the odo display...