Depends on the roof configuration and the size. Remember this is a tech company doing construction work probably using subs in an extremely tight labor market. I would not be surprised that they bungled this initially. Elon suggested such in the article. Of course as I've said the specifics will remain unknown so people are free to make things out to be worse than it was or less so.Wouldn't they know that happens regularly.
Seems ludicrous to me that they knew nothing about their job.
Besides stripping a roof down to trusses, resheathing and shingling it, doesn't cost $40,000 on a house, not even a large house.