Exactly. The tricky part is that board started a second for profit company with VC investors who are co-owners. This has potential for messy conflicts of interest if there is disagreement about how to run the co-venture, and each party has contractual obligations to each other.
Anyone investing in or working for the for-profit LLC has to sign an operating agreement that states the LLC is not obligated to make a profit, all investments should be treated as donations, and that the charter and mission of the non-profit is the primary responsibility of the for-profit LLC as well.
OpenAI employees might not like it and it might drive them to leave, but they entered into this agreement with a full understanding that the structure has always been in place to prioritize the non-profit's charter.
Which might only be possible with future funding? From Microsoft in this case. And in any case if they give out any more shares in the wouldn’t they (with MS) be able to just take over the for-profit corp?
However, to nitpick your nitpick: for non-profits there might be no other party - just the mission. Imagine a non-profit whose mission is to preserve the history and practice of making 17th-century ivory cuff links. It's just the organisation and the mission; sometimes the mission is for the benefit of another party (or all of humanity).
I can see where the misalignment (ha!) may be: someone deep in the VC world would reflexively think that "value destruction" of any kind is irresponsible. However, a non-profit board has a primary responsibility to its charter and mission - which doesn't compute for those with fiduciary-duty-instincts. Without getting into the specifics of this case: a non-profit's board is expected to make decisions that lose money (or not generate as much of it) if the decisions lead to results more consistent with the mission.