> Of course there's a huge risk of it becoming made for-profit.
The article says that "it will become an independent nonprofit corporation", and as OpenAI's failed attempt showed, converting a non-profit to a for-profit organization is either really hard or impossible.
> Could they not have made it into some legal structure that puts universities at the top?
As a corporation (even a non-profit one), it will have a board of directors. I have no idea what their charter will look like, but I would be surprised if at least one seat wasn't reserved for a university representative, and more than that seems quite likely as well.
Is your argument really that "OpenAI was an independent nonprofit corporation and it worked out great, Arxiv will remain just as non-profit as OpenAI"?
OpenAI didn't get everything that they wanted, but I very much disagree with calling it a "failed attempt". The non-profit went from owning the entirety of OpenAI to having ~25% stake.