It's a mess for sure. As I understand it, the developer included the # of required spots when the building was built.
They then "sold" rights to park in the garage as part of specific units (SF requires occupancy of 2 of more in order to qualify for parking so not all units got a space).
Once all units in the building sold ownership was transferred to the Homeowners Association who is responsible for accommodating residents with garage access as needed. Since it is a private gated garage the Association manages swapping spots as need to accommodate anyone who is or becomes disabled. Or at least that is what the governing documents the developer provided laid out. Sounds like this has a high change of turning into a circular firing squad of residents sueing the association, each other and the developer.
I guess it shouldn't really be a problem as long as the disabled spots are assigned to, or being used by, residents with disabled license plates or placards.
I thought illegally parking in a disabled spot would mean immediate tow and extra fine, like $1000?
It could be towed, but probably not normally. The minimum fine for disabled parking violations in California is $250. It can be more in some jurisdictions, but I don't think anywhere near $1,000.