Last time I played (probably a year or so ago) I named her "mom" as well and that worked. However, since then other characters have been introduced and in this update, the Aunt called her "mom" too.
As stated earlier, it's a shitty, immersion-breaking method. Either you call her by her first name or other characters will also call her mom.
Some devs lack common sense when it comes to this kinda stuff.
I have not played this past the very early game yet, but I'll bet my left nut that the story does not make any sense with landlady and roommate. There is no family dynamic with your landlady. She will not raise you like a son since childhood for no reason. You pay rent to your landlord/landlady, that's it. If it was something like a family friend who took you in after your parents passed away, it could make sense, but that would require actually wriing a proper backstory. It also has it's own problems with user defined relationships.
There is a mom's name variable. Lets call it [m_name]. There is a mom's relationship variable, say [m_relation].
Let's look at a very basic example.
"Good morning, ____. Did you sleep well?"
If you use [m_name], it will make sense for the landlady (ignoring that fact that you are living like a son with your landlady) and family friend dynamics. It won't make sense for the incest relationship because you will not call your mom by her first name. If you use [m_relation], it will make sense for the incest, but not for those non-incest relationships.
You can write around this occasionally to make things work for both versions, but more often than not, it will not be possible and just the fact that you have to constantly worry about it is a constraint on writing (unless you just don't give a fuck about it like this dev).
You have to sacrifice either the non-incest or the incest version when using "word replacement patch"/"user input systems." So which route do we sacrifice? Well, the answer is painfully obvious. No one (hyperbole, I know) is playing this shit with landlady and roommate because that dynamic makes no sense in this story. This is an incest story, so when deciding if you want to use [m_name] or [m_relation], give preference to the way that makes sense on the incest version. Saying, "Good morning, Landlady. Did you sleep well?" is a small price to pay to get rid of the immersion breaking script on the incest path, which is obviously the intended story for this game.