The othe option to the Merryweather Heists also has the red X's, 2 of them but, here is the wierd part...
when you are Michael swimming up to the weapon the X's are right by it but, as soon as you get too close it initiates the cutscene of him marking it and then the game switches you over to Trevor.
this is when the red X's move position, one moves in front of a JetSam shipping container and the other X moves in front of the big hole in the side of the boat..... and there are JetSam containers in there...?
The THIRD X(did i forget to mention this?) is just where you would expect to find it if you were looking at the RIGHT side of the mural and rotated 90degrees counter clockwise.
That's right, the 3 X's match up to the X's on the right side of the mural.
unfortunately cant take pics underwater(curse u R*!) so pics are hard to come by of these tings.