If you're having custom cabinets installed, no reason they can't make the uppers a couple inches shorter if you want your full 18" between countertop and upper cabinets.
You could prolly learn to live with the 16", too.
Your half-inch subfloor is no subfloor at all to my mind. If you've got a height problem, I'd start by removing that subfloor and starting with a minimum of 3/4" T&G plywood and work up from there. Using a membrane such as Ditra from Schluter or one of Noble Company's products could save you a little more height.
My opinion; worth price charged.
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