I have had similar issues with my 1999 ES300 for the last 5 years. Although not the extremely frustrating issues your wife is having. I wake up to dead car not hands full of shopping bags dead car.
2 batteries and 3 alternators have been sacrificed.
Fortunately the alternators from Autozone are lifetime warranty so the Autozone tech does a test and I just change it there in the parking lot.
I am almost positive it is some sort of parasitic draw but have never tested it (today I am, thanks for the vid link).
When you first start the car interior lights and daytime running lights will kind of "pulse"; not strobe light speed but a slow 1, 2 dim, 1, 2 bright 1,2 dim, etc. I hope I explained that clearly.
Should I try to find a higher quality alternator instead of the autozone brand?
Regarding alternator power output: Has anyone used Torque smartphone app
and Bluetooth dongles
for voltage measurement?
How accurate is it?