A flush should not be that surprised on a paired board. A player is not likely to put it all in without quads, boat or a big flush. There are a lot more quads plus boats than big flush. With a flush on the board they are not as likely to bluff.
On a paired board your opponent has a boat or quads with any of 4 pair. If the opponent is not paired there are 2X9 = 18 hole cards that would make a boat.
There are just over 1 million paired boards so versus a random hand only like 0.002800%. But you cannot go with that as you are not facing a random hand here.
If the villain calls the flop and turn and jams the river then hero needs to think twice about a call. Hero should not be surprised when villain shows a boat.