That seems to fit:
1.) move from Palo alto to east bay
2.) manufacturing company with software engineers
3.) lots of people leaving
4.) CEO changing the world.
Bingo. The company was Rocket Science Games. https://web.archive.org/web/20121113115319/https://engineeri... says Blank was involved, and one of Musk's internships was also there according to the Musk bio and a few sites listing his internships (simultaneous with Pinnacle, apparently).
That really makes me feel old - I used to work for another gaming company at that time that was pals with Rocket Science. It was not exactly a model of how to run a business - and where I worked was hardly GE. :)
From dubious acorns doth startup management gurus grow.
While it may fit most of the criteria, I wouldn't say Martin Eberhard and Marc Tarpennin were the visionary founders mentioned and Elon Musk and company tried to bring in adult supervision before Elon sunk enough of his own money into the company to just start running it himself.
Most of the narrative doesn't fit as this article presents it ( it might still be tesla, but you can assume the details are pretty one sided )
My guess is square. The CFO went to stanford for an MBA, where the author taught.
Neither CFO Tesla has had went to Stanford.
Can't find anything about Dorsey working at one of the startups listed on the author's wikipedia page, but he seemed to have been involved with many so it would be unsurprising if it just wasn't listed there.
I worked at Square on the hardware team. Sarah Friar (CFO) and Jack Dorsey (CEO) aren't like that and Square doesn't do any manufacturing. They use contract manufacturers.
Square was never located in Palo Alto (although there is/was a small South Bay office where people could work one day a week) and is not, as far as I know, moving to the East Bay.