We've had similar issues with previous and our current boat... closing the through hull is simply part of the 'presail' checklist. In case the through-hull doesn't fully seal under pressure, HyLyte's stopper sounds like a good idea.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)