The relation between a son and a mother, and a man and his landlady, is hugely different. The interactions would be drastically dissimilar and so the story could realistically diverge in much different directions.
Exactly, the interactions are assumed to be drastically dissimilar. Therefore, they should be at least a bit dissimilar in order to make sense, don't you think ?
The context of the game will itself be fantasist, so that the landlady act like a substitution mother will not feel too odd. I'm sure that remembering your youth, you'll find one woman, a neighbor or friend's mom, who was always motherly with any young she interacted with. This "oh dear, it's too cold outside, you should have wore a coat"/"you're so pale, let me check your temperature quickly"/"I hear your parents are out of town right now, tell me, you don't only eat on pizza, right ? It's not healthy at your age you know" kind of woman.
But it will not feel too odd as long as she don't totally forgot that she's the landlady. And it's what happen with games where the patch is limited to "enter how you call her" kind of questions.
That she never talk about the rent, no one will really care. But that she start giving some pocket money, seriously ? That she feel too close to you to engage in a relationship, why not. But that she argue that it's because it's your landlady and one shouldn't have sex with his landlady because it's not moral, what the fuck ?
In most games, it would never be more than a hundred dialog lines that would need to be changed, over dozen of thousands of dialog lines. And if you planed your story to take those difference into account, only a dozen of lines would need to be changed ; the one related to her motive to initially refuse to engage in a relationship with the MC.
It's not something big, but it will make a big difference for the players ; the same kind of difference that an ambidextrous tool make for left-handed. The author of the game cared about all his players, making a game they can enjoy whatever if they want to play the incest version or the none incest one.
Edit:
So if we take that to be true, that having the ability to choose another relation to the mother means that the gamemaker has no writing skills and the story is instantly cheap, the question is: what's then the alternative?
I said it, with most game engines it's not too difficult to replace a sentence by another one.
Make sure the landlady do not act as only a mother would do, and for the few case where you can't, at least have two versions of the key dialog lines. One that apply to the mother, and one that apply to the landlady.
Mother "You're really a lazy ass ! Never leaving your room, except at lunch time.
I'll not pay for you all my life, you need to find a job else I'll
kick you out of the house."
Landlady "You're really a lazy ass ! Never leaving your room, except at lunch time.
You don't live here for free, you need to find a job else I'll
rent your room to someone else."
Mother "
Hey, son, you behaved recently, here's some pocket money, use it as it please you."
Landlady "
By the way, there were this with the last payment your parents did. Since there's no instruction, I guess they want you to use it as it please you."
Mother "No, we will not shower together !
I know that we did it in the past, but you were a baby at this time. It's really inappropriate for an adult son to shower with his mother."
Landlady "No, we will not shower together !
I don't care that you did it with your mother when you were a baby, we don't have this kind of relationship, period."
Mother "I get it, you're young and horny every time, and for whatever reason you think I'm more beautiful that girls your age.
But no, we will not have sex ! I'm your mother for god sake !"
Landlady "I get it, you're young and horny every time, and for whatever reason you think I'm more beautiful that girls your age.
But I'll not have sex with you. How inconvenient it would be, you live under my roof since too long don't you think ?"
And so on.
