Disagreement between 4 sources here:

1. Mini Specialist in San Diego: Checks with multimeter across the battery while running, Shows 12.5-13.5 volts. Advises me to take car back to the place that replaced the voltage regulator and have them replace it under warranty.
2. Independent shop: Tests using autel meter. Alternator checks out ok with no load voltage of 14.18 and load voltage of 13.6.

Car still has a stored transmission code so they advise me to take it to the dealer to troubleshoot that. ​​​​​​
3. Mini of San Diego: Charging system OK, resolves transmission code issue by cleaning fluid out of connector.

So today I take the car in to get it smogged and it starts doing this crazyness again and goes in to limp mode.

I pull over and check voltage on the jump point and it's 12.5V with the engine running.
Take car immediately back to the independent shop and the alternator checks out fine again.

4. I double checked the Bentley manual and they say you can just check with a multimeter across the battery posts.

So why are the more sophisticated tools saying it's ok but the multimeters say it's low?

At this point we're suspecting a bad ground or some kind of short but that's another project.

 

[Edited]
First
>the Stealership
No, just no. As in not even once.

Would see if the transmission code came back and recheck that connector. And why was there fluid on/in it? Leak? Transmission control module is on the same bus as the instrument cluster (speedo) which is linked to the tach. If there is an issue(s) with the transmission module, would suspect it could be playing hell with the other two. Could also be that the tach / speedo are going out; my tach exhibited similar behavior of dying / coming back life, then lights staying on after key removed, etc. Replaced it with a 'known goody' from Evilbay, no further issues so far. Ref: Bentley chapter 600.

If the last thing done to the car was the VR, would consider pulling the alternator and battery, have both tested at local brick and mortar parts store.

 

The variable readings can arise if the alternator/voltage regulator is acting up. Have encountered this a couple of times over the years with cars of other people. Then had a car do this. From a cold start and for some minutes after everything was fine. Then I noticed the battery voltage gauge was reading lower than "normal". Remembered what I had observed before with other cars and suspected the alternator was acting up. Headed car towards my dealer and as I drove the voltage level dropped to the point it appeared just the battery alone was supplying electrical power to the car. I had of course turned off what electrical loads I could when I pointed the car at the dealer. Thankfully it was day time so the headlights were off.

Tech diagnosed a bad alternator/voltage regulator. Upon cold start the alternator output was fine but after a few minutes was not fine.

 

The leak is apparently coming from the valve body down the cabling into the connector.

They wanted like $5k to do it. The car actually had a transmission rebuild last year so I asked the shop if the valve body was new and they said no because the valve bodies are something only the dealership can handle.