That would enclose the 3/4" plywood and laminate? If they do, you'll have a 1/4" of the new sub plywood showing, below the fiddle. If so, you could cut increase the rabbet to 1" to cover the ply and Corian.

If there is no rabbet, then, no problem! Either way, you lose a 1/4" of fiddle height as you mentioned, unless you cut new ones.

I would bet the fiddle will be easy to remove once you get the screws out. If they used adhesive(I doubt they would have), it probably isn't that much of a bond on the edge of plywood. If it's in good shape, I'd be inclined to re-use the fiddles, I bet you don't miss the lost height.

My old boat has a very small fiddle in the SS trim piece, 1/2" maybe. But the counter runs athwartship, so it's enough. Good luck, and post a pic when you get it done.