My objection is that Features are codified, and presented as interchangeable, when they shouldn't be. If your character backstory is that you're a noble, then it's already true within the game world that you are a noble, and you shouldn't need the "actually a noble" Feature from the Noble Background in order for that to be the case. If your backstory doesn't include that you're actually a noble, then it's not true within the game world that you are a noble, and nothing written on a character sheet should be able to override that.
If you want to be a noble who became a pirate, then that's who you are, and people will react to you accordingly. You shouldn't be forced into choosing between the Feature from the Noble and the Feature from the Sailor Variant: Pirate, when both choices are equally valid and neither is quite sufficient.
Well, you aren't forced to do that. You basically have three options (as I see it) - decide that based on your backstory the Pirate background is what best represents your character when the game starts and use the background feature from that (you are a former Noble, but no longer benefit from the social status), or decide that despite your recent experiences as a Pirate, you are best known for your Noble status. (So you don't have the pirate bad reputation, but you do have your noble stats). Or option 3 - decide that neither of those fit your character and work with your DM to create a new background feature that does.
The listed backgrounds are the starting point, not the end point. This should be a fun part of character creation, not something to argue over.