Makefile.install uses MAX_THREADS when writing the pkgconfig file, and falls back to the build host core/thread count when "NUM_THREADS" is not passed to make install.
NUM_THREADS is not written to Makefile.conf_last, contrary to e.g. DYNAMIC_ARCH. This is probably an oversight.
There are other options which apparently are not saved when building the library (i.e. everything related to install directories), and are evaluated by make install/Makefile.install, but there is unfortunately no documentation when each option is evaluated - by make, make install, or both.
It is probably save to pass all options to both calls, but this is not what the current documentation suggests or uses in the examples.