There is so much wasted/poorly optimized land in SF. I cringe whenever I see the massive surface level Safeway parking lot in Duboce/Church.
One easy to appreciate example are universities & other schools holding (& sometimes leasing) land adjacent to them. If they didn't, in the distant future if they need to expand, some scalper or holdout could cause large problems.
And as a consequence of the old adage "time is money", an indefinitely existing organization has an indefinite amount of money. Those institutions you mentioned have no issue buying whatever they want; holdouts be damned. A government pretty much has infinite money, churches are quite wealthy as a whole, and universities have a substantial pool of donors to tap despite having insanely large endowments that are quite well managed.
I don't think your argument holds up.