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.
1984 Fast/Nicholson 345 "FastForward"
".. 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)