Could they not have made it into some legal structure that puts universities at the top? Say, with a bunch of universities owning shares that comprise the entirety of the ownership of arXiv, but that would allow arXiv to independently raise funds?
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.
So if OpenAI with billions of dollars only partially succeeded at converting to a for-profit business, then that suggests that organizations with fewer resources (like arXiv) have much worse odds.