Can confirm that the yellow "Q" is still in use everywhere.
I believe the vessels registry determines the flag flown aft (not on a pigstick, as T34C pointed out - they are for YC burgees)
My guess would be Red Ensign rather than the Union Jack as a courtesy flag. Perhaps fly the others mentioned below the Red (or on port side?) if you are in those regions? Not sure about that either.
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)
1984 Fast/Nicholson 345 "FastForward"