Yeaaaaah... there were some odd storytelling choices with this one, breaking its own internal mythology rules several times, throwing out anti-climax conclusions all over the place, enough handwaving to give yourself an RSI, and most unforgivably, the manga itself is tagged for Yuri as a whole, when it's only really applicable for a couple of chapters in the middle with the pirate ladies show up.
The tags should really be amended on this one, so people know before getting into it that the gay has been quarantined to only those few chapters, and comprises the "gay villains who die" archetype. Classy.