i think it goes back to the story you've been telling up to that point.
personally, i really hate the 1/3 river bet simply because it seems to rarely have fold equity when bluffing.
as for the OP, yes, i often bet full pot on the end if i backdoor a flush simply because people don't believe it. that being said, i bet full pot other times, too (a bit different in plo8 due to the split pot nature), and my "value bets" are often 2/3 pot or larger.