MQTW is based on either flap 30 or 40, both tables exist.
However, be careful and look into your AFM (should be on the aircraft), as the MQTW requires 67 minutes of cooling time for the 737-800 for instance. Most operators do not have such turn around times, thus the MQTW is slightly arbitrary.
Regarding cooling, yes the brakes need to be released to allow airflow around the stators and so on, this is the medium after all which absorbs the heat from the brake assembly.
See
this presentation for a Boeing FLOE explaining the works! You could be surprised...