I thought the universities were still government owned?

This is a really good question. My understanding is they are self-owning (thus “autonomous”), but because they are incorporated using a special legal structure just for them - rather than being incorporated as a company or trust - this gives them special status as a “Crown entity”. It’s vaguely analogous to the special legal structure that iwi use to incorporate, for purposes of receiving and managing assets received as Treaty of Waitangi settlements. The iwi aren’t state-owned, but in a sense they are a special sort of “Crown entity”. I’m not an expert of any of this stuff, just a longtime observer, so I’d love to be corrected by someone who is.