You’ll need to load the master sequence into MRQ. It should recognize your shots and then you can disable rendering the other shots if you wish.
You can also load that shot into MRQ by right clicking on it in Sequencer and choosing Render Shot (that will load the master and disable the other shots).
Either way, MRQ needs to see if from the perspective of the master sequence.
(Alternatively you could restructure it so that you put the subsequence in the shots, but then you’d have to offset it inside)