It isn't set up for the main character to be the only dick around, as that would be rather unrealistic. He is however the only fertile male left aboard the ship.
The "ending" will be story-based and not focused on what girl(s) you end up with. That being said, you will end up with who you end up with depending on who you choose to pursue. Essentially the ending of the game is based on the plot, and not what girl(s) you pursue. All of the girls will be there throughout the course of the story whether you have sex with them or not.
Thus far none of the women start out claiming an exclusive relationship with the player. That's something that will need to be built up by playing the game. There isn't any NTR so long as you don't automatically assume you somehow own the women in question before putting in the work.
Each woman has a unique background and a personality we hope has depth to it. They are independent actors in the plot, not just objects to collect, if that makes sense.
All this being said, you can skip NSFW content with Persephone by selecting to turn off M x Futa content in the menu, and/or by making the appropriate dialogue selection in the game. You are not forced into viewing or interacting with the hermaphrodite character in any sexual way. She will not be removed entirely from the game though, as she is an important member of the Desperation's crew.
I hope this helped explain.
-Pelorix