My reading of it is the school over all is better/more conservatively managed than GTAA. Comparing athletics to the overall university is (according to this writer) a way of normalizing the numbers to better gauge the AA balance sheet.
Dumb question: Could GTAA go bankrupt without the university providing some kind of backstop? I just did a search and found no cases, so must be nearly impossible, which I suppose means the AA and university must be somehow intertwined (but how?).
Regarding endowments, they are targeted for very specific uses, so to move the money you have to go to donors and get written permission (I know this first hand, having done it).