Yes, it’s standard practice to spray clear over the binding. You don’t have to, and I know a few people on the forum kept the bindings taped up. If you don’t spray over the binding you’ll probably get a step round the edge of the binding. The clear coat is a very good way to remove any height difference between the binding and the body.
With a bound neck, the common practice is to spray clear over the binding on the sides of the neck, but to keep the top of the fretboard fully masked and to scrape off any clear that creeps under the edges, so the upper binding surface sits flush with the fretboard. Spraying over the binding on the side is another way of ensuring a smooth transition between neck and binding. Any ridge here can feel awkward under your fretting hand.