Apart from the facts (that program managers have left), the tone of the whole article feels like that this writer absolutely dislikes Musk.

Sorry, I didn't mean tone as in "dislikes Musk", I meant tone as in "unreasonably dislikes Musk".

makes one really wonder how the writer came to dislike Musk of all people...

If they're claiming to be a journalist, their personal feelings on Musk should be irrelevant to the story.

The heads of Cybertruck and Model Y programs are "low level"?

He wasn't the "head of cybertruck" - if you look at his LinkedIn, he was a lead program manager. Still an important cog in the machine, but he'd been there for 8 years from an intern.

Model Y guy makes it sound like he was more of a key person, though.

More like not important, Tesla was never a car company /s