You asked for pirate comic pushback, and here it is. The comic-within-a-comic is not merely there to provide ironic counterpoints to other dialogue and events, but can be read as foreshadowing of the larger story and the person responsible for almost everything in it.
First, the protagonist of the story isn't a pirate. He's the lone survivor of a pirate attack that wrecked his ship and left him marooned on a small island, and is referred to in the back matter as the mariner.
Second, his single-minded determination to escape the island and warn his coastal village of what he perceives to be the impending attack of the pirate vessel is meant to mirror one of the WATCHMEN character's single-minded drive to save humanity from what he perceives to be its impending doom.
Third, both the mariner and the WATCHMEN character go too far in their respective pursuits, resulting in multiple unnecessary murders.
Finally, at the climax of the pirate story, the mariner discovers that his fears of the Black Freighter's slaughter of his family and friends were unfounded and that he's the cause of the very calamity he hoped to prevent. He sees the Black Freighter sitting in the harbor and swims toward it. The WATCHMEN character has dreams of swimming toward something hideous and almost reveals them before catching himself, but does he really feel any guilt for the millions of deaths his actions have caused, or is it just for show? (Ironically, this is for the benefit of a character that has already lost all touch with his own humanity, rendering the effort to present guilt meaningless from the start.) Does he truly feel as damned as the mariner did in the story?
My opinion is that he doesn't, but Your Mileage May Vary. Furthermore, I would argue that by setting certain specific events in motion, he would have been responsible for causing a nuclear war that would not have happened but for his murderous machinations. Again, YMMV.