The type of flush I was referring to is the ones they do at a quick lube, why bother flushing out the fluids and not changing filters, your only leaving the mess behind.
IF the machines used by such service stations are NOT maintained and cleaned they can cause contaminates to enter the transmission, possibly being collected in the filters but further reducing the filter lifetime ( which is most likely exceeded already ).

I had already conceded that using the pump to drain is acceptable and NOT THE SAME as a flush in my mind. As the op plans to change the filters and continue to pump out the fluids until clean.