So I follow the directions regarding bench bleeding - my M/C came with little plastic fittings & hose supplied - nice touch!
Step 1 is no problem - remove the output fittings that go to the PPV and replace with the plastic fittings & hoses which are routed into the fluid.
Mission accomplished - got all air out & the unit is bled with the hoses into the reservoir.
So what then - you just disconnect the plastic couplings and refit the lines to the PPV?

I assume purpose is to ensure there is no air in the cylinder - disconnecting the output will drain fluid after that, but as long as the opening port remains submerged, there should be no impact to the cylinder - is that correct?
When I go to bleed complete system, I have a vacuum bleeder incidentally. Makes life really simple - was a good investment.
I have the MightyVac brand that operates off a venturi from compressor