I harvest yeast via racking arm so I am pulling the middle slurry of yeast. If I have to go from bottom port I do dump dead yeast and trub before collection. That said, I still homebrew and reuse yeast and jump harvest the yeast in mason jar and go with what I have, no rinsing, no separation. Doesn't seem to make any difference in beer clarity.
That said, on both homebrew and commercial set up I leave most of the hops and trub behind in BK, which I do personally advocate. I whirlpool and have a plate in front of my exit port to hold back most of the hops and trub.