This is a problematic way to simulate incest. If we are changing her literal name to "mom." It puts so much constraint on the script to accommodate this type of incest "patch."
Think about it, how will other characters than the MC and sister call her? Your neighbors will call her mom? Same thing goes for the sister. If you change her name to "sister," you have unnatural dialogues between siblings, who normally don't refer to each other as sister or brother. The mom will call her sister too if you call the name in the code for her dialogue. If you go out of your way to accomodate the names literally being "mom" and "sister," you have problems for non incest version of the script. "...but I'm your mom..." Will turn in to "...but I'm your Jenny..." Something like that.
As you can see, the best option is to make an incest patch with an actual revised script that incorporates incest because simple word replacement really doesn't work very well. If you are insistent on using the user input method, at the very least, you need to give them actual names and let the players input the relationships.
So I'm not sure if the solution was solved, I never coded a game before(but I do know coding) and I haven't tried the game yet(going to) so I'm not sure what is the script is at the moment but what if there is an option to click: "related". Then you name the character as mom.
The idea is that when the related checkbox is ticked, any dialogue involving narration and reference from other npcs would include a Your in front, while excluding player's dialogue.
Something like:
"Related" checkbox:
Ticked
Name: Mom
Npc: Your mom is a red-head
Narration: Your mom has green eyes
Player: Hello Mom
Thinking: Mom braided her hair today
"Related" checkbox:
unticked
Name: Mom
Npc: Mom is a red-head
Narration: Mom has green eyes
Player: Hello Mom
Thinking: Mom braided her hair today
Would that help? Plus having the checkbox tick can tell the codes to add or exclude any dialogue that is relevant if the character are related.
"Related" checkbox:
Ticked
Mom: Hello son, your dad left us.
Mom: I know it wrong but I want to fuck you.
"Related" checkbox:
unticked
Mom: hello player, your dad left you under my care.
Mom: I am so horny that I want to fuck you.
Still, at the end of the day, based on what others say and based on past project from other dev., you alone should determine the story's narrative and not try to please both side. If it is incest, make the story with incest in mind. If it isn't, then make the story where they are your caretaker.
Fan's suggestion or other external influence should not change your original story BUT instead enhance it by suggesting to remove or add certain dialogues, viewpoints or scenerios so as to improve the story telling or reveal certain information without outright telling it.
It should not be like: suggesting if the Mom shouldn't die because it is their favourite character and stuff like that.
I know it not fair to you as I can easily say this with no consequences, while you need financial support. It is also best for you to get as much income from both side to fund this project. But as stated, based on many people experience, the playerbase tend to hate it when the story is ruined by creating a general story plot that tries to please both side but fails.
Anyways, I'm gonna go play your game now, I wish you success and I hope atleast at the end of the day, you manage to finish the game and not abandon or milk it.