I play without the patch (I'm not a fan of incest) and I didn't find it odd. I assumed that the Mom and Dad have been split up for years and/or the mom has known her for years and is cool with her. I don't know if they address it in the game but The MC mentions that he isn't close to his Dad and I got the impression that they hadn't talked much or seen each other much over the years.
The dialogue for the non-incest variant to this one is handled a little better than other VNs I've seen. You could tell the dev (at least early on) tried to make both variants make sense. Portraying the aunt as
an old family friend with a daughter can make sense contextually right up until the part where Elly's relationship to the MC is revealed and the MC acts like they did something taboo. There's obviously nothing controversial about fucking a childhood friend but when the dialogue shifts into taboos like "
But it was so wrong! You're my _____!", then it makes it pretty obvious what the canon relationship is really supposed to be.
I don't care about incest one way or another so I usually start VNs without incest patches. Regardless of my feelings on incest in the real world, in the AVN world it's such a common trope that it's almost a rule at this point. Like "
If thine family members are hot then thine family must be plowed". However, I prefer dialogue to make sense in context and the moment there is any hint of a taboo in the dialogue, then I'll toss in the incest patch so that it makes sense.