A few things.
1) The epiglottis has nothing to do with closing the airway. It's a tissue flap that helps prevent aspiration of food and saliva, but a minor player. It's possible to learn techniques to swallow without it (such as with people who have had the supraglottic larynx removed for cancer). It occasionally can cause minor airway obstruction on inhalation in babies because it is soft and floppy in the first year of life, and curled on itself (laryngomalacia). This is rarely seen in adults, and usually only in patients with neurological disease.
2)The vocal cords (glottis) coming together (adduction) is what makes an airtight seal of the airway. From an evolutionary point of view, that's why we have a larynx to begin with - speech is a later benefit. Because non-cetacean mammals have crossed air and food passages, we need some fancy reflexes to shut the vocal cords and keep us from drowning in our own saliva, or every time we take a drink of water.
3) Forcefully adducting the vocal cords while ascending is what causes pulmonary barotrauma. If you aren't doing that, but are just pausing breathing, then the expanding gas in your lungs will vent on ascent.
4) Getting back to the OP, my understanding of "surge" is that the volume of water that you are suspended in is moving up and down. Therefore, surge should not change your actual depth at all, and you should be at no risk of barotrauma. There are stories of people doing deco in heavy seas, where the waves were big enough so that divers at their shallow stop could actually be seen at deck level, but inside a wave adjacent to the trough that the boat was in! Not sure if that is apocryphal, but you get the point...