Just one point in the article.
"It’s also caused disquiet because it was funded not from donations, but by a restricted grant from the Knight Foundation. "
Now other than references to KITT, having restricted grants in the charity sector is pretty common place. For example, I help run a youth club and it's not uncommon to get grants / donations for "Only to be used for a youth worker" or "must be used for an art project". A good many donors also put caveats on that the details of their donation are not to be disclosed to the public.
So to infer this is some dark and mysterious act, may be something as simple as "we want a better search engine".
Now some people find this odd and go, "well why can't we use it for XYZ" and get the hump, but as it's a condition of the donation, you morally, if not legally, have to comply.