No Choice
Actually, you have no choice! By sanding down to the gelcoat, you have probably already sanded away a little of it. And, most of the gelcoat's ability to seal out water on the molecular level is in the outer 5%. Lots of boats get blisters when their owners, meaning well, sand the gelcoat to apply paint. AT this point, you are not dealing with the same gelcoat barrier you started with, so, IMHO you ought to go ahead with the barrier coat. You will wind up with more protection than you started with, and your boat and you will thank yourself for it down the road.