I believe if you use the original cove as perscribed and taper the foam board against/overtop, and do two layers, you end up with your cove burried or partially burried and not doing what it's supposed to do.
Since you have a granite base with irregularities, unless i see it, I'm guessing, but what it boils down to is:
Will one layer of board burry everything that could possibly damage the liner sufficiently enough that it will not poke through? If yes, use one layer, if no, use two.
Any which way - put the cove on top of the foam board, if you go underneath, like stated in posts above, a gap could develop and the cove is supposed to cover/seal any gap potential. does the cove just have a slit on the back for cliping purposes, if so, I think you can still use it successfully.