My manual says the same thing, don't run the motor on the flush port. That said, our local mechanic doses it all the time on Yamahas but then again, he is also the guy making a living changing pumps
That hose diameter on the flush fitting is really small and it can't see it move a lot of water.
I add a quick disconnect fitting kit that I find at Lowes. It has two different combos of male/female. One never gets used!
I add a similar fitting to my garden hose and a fitting to my nozzle. To flush, I just pop off the nozzle, unclip the fitting on the flush hose and plug in the garden hose. It's fast and easy.
Downside: The spring in the quick disconnect fittings only last two seasons due to salt air and water.