Seems pretty straightforward... Elon invested when they claimed to be an open-source non-profit, and clearly now are closed source and very for profit. The notion that the for profit is just a temporary means to achieve scale goals is laughable.
He claims he'll give all the money to charity, but he's certainly asking for money.
2) Lots of non-profits make a profit. A non-profit is not defined by losing money, it is defined by the nature of what it does with its money, and what parts of its revenue are subject to taxation and what parts are tax-free. For example: the Microsoft contract would have been subject to income tax even if was directly with the OpenAI non-profit entity; moving that to the for-profit subsidiary just simplifies the accounting.
3) I do not think that OpenAI's mission should have ever qualified it for IRC 501(c)(3) status, but the IRS didn't agree and at this point it would be very difficult to challenge the (parent entity)'s non-profit status.