The dedupe job can run alongside 'normal' volumes of incoming donations. However, when emails go out the backlog spikes up to some thousands. I am adding the following options to the drush command

--threshold=1000
--threshold_period=5

If a threshold is passed in then the job will early-exit if more contributions than the threshold number have been imported in the number of minutes specified by the period (optional, default 5).

If no threshold is passed in then no threshold logic is applied