Isn't this normally done with a GPIO bootstrap?

It depends. Usually there are enough "knobs" that adding that many balls to the package would be crazy expensive at volume.

Most SoCs of even moderate complexity have lots of redundancy built in for yield management (e.x. anything with RAM expects some % of the RAM cells to be dead on any given chip), and uses fuses to keep track of that. If you had to have a strap per RAM block, it would not scale.