There is a reason it modifies all scripts, adding/replacing you still get your father, your step-sister, there isn't any real incest, that's why the patch is re-written...to make it family friendly...and actual more lines are added to make it fit.
I mean to say that throughout the dialogue it clearly says she is not your mom and you are not her son, even if you change Sophia to Mom, it doesn't make sense when you actually play the game itself.
Hi, Mom, you are my dad's girlfriend, and this is my step-sister, and she is your daughter... that is so much better and totally makes sense doesn't' it? What a fucked-up family.... later on in the story, it even says they are not related....
There is no incest in the game even if you change Sophia to MOM since the diallage will even say she's my "Dad's girlfriend" , she will also say this is my daughter, but not your sister...
That's why it modifies the entire script, there isn't any incest in it all. I had to manually go through the script and edit line by line, and each release it seems like the dev does a different format, which makes previous patches null in void.