Same reason we do today, they’re cool. https://en.wikipedia.org/wiki/Gateway_Arch

There’s one hell of a lot of people go through the same kind of thing you’re going through, and it’s not fucking easy. If you don’t fit the ‘default’ settings for the world, many people will struggle to communicate comfortably with you, and that can feel annoying to them.

Going through such a tough childhood no doubt instilled a lot of coping strategies that can be hard to overcome, and which may make it harder for you to accept yourself as yourself, or to look for solutions to certain problems. If you’re able to find counselling or a therapist, do, and try a couple different ones because they need to be able to connect with you.

If you’re able to stick around, you will, sooner or later, find a group who are your brand of crazy. Who won’t get annoyed at any quirks you may have. It’s worth looking for these groups, even if you look online. It’s also possible that you find your group or groups change over time. It can be sad to lose friends as you all find a different path in life, but the diversity of friendships can be part of the beauty and wonder of a full life.

I should say, the trans side isn’t a quirk, that’s just who you are. You are experiencing, it seems, some of the bodily concerns that many women, including cis women, have been fighting for decades, specifically with how women are expected to look. Take the Olympic boxer recently who, despite being a cis woman, is being shamed because ‘they’re clearly a man’. Bullshit, they’re not even trans, so if people can’t tell that someone who’s born a woman is a woman, they’re going to completely fail to identify anyone else’s gender. Gender is a very personal thing, so the only person who gets to judge that about yourself is you.

From my limited experience, NPCs come in two varieties, persistent, and instanced. An instanced NPC is a bandit on the street who, if you kill, will drop loot, and then never affect the game ever again. They appear and disappear as easily as a glitchy texture. A persistent NPC, you will probably want to track more of, but even then, you don’t have to track everything.

A shopkeeper, you may generate their shop inventory when the player loads the area, but then clear it when the player leaves the town, or a certain amount of in-game time has passed. Same with aggression responses, you could have a list of NPCs who are unhappy with the player, and after a while, they’re removed from that list. No need to store the NPCs dynamic opinion on each NPC, just that they are unhappy and when from. When you load the area, you check that table, and the NPC reacts accordingly.

Maps, you’d want to do region by region too. Of course you’ll need your data files, terrain, navigation maps or whatever you need, but for the most part, you can choose to only store changes. This means you don’t store the whole region in a file, only which containers have been looted, what persistent NPCs have been altered (enraged, seduced, quest actions completed) and such like.

Player stats… yeah, surely you need to just store those in the save file and assign them to the player object. Level up, when you reach the level up conditions, you get to improve. How that works is entirely down to you, the dev. Don’t be afraid to play around and see what works.

I’m sure there will be other people with far better advice, but this should help guide you in the right direction.