This game immediately falling victim to user input relation problems. Nothing makes sense. Lisa's parents died. Ok that's canon so Sharon cannot be her mom. Game tells you she is her mom's friend. If we ignore that and enter Aunt, Lisa just refers to her by her and the "uncle" by their names. If we use the default relations, it will be landlady, landlord, etc. That doesn't work either because mom's friend taking you in doesn't make her your landlady/landlord. The relationship dynamics wouldn't work because they don't act like landlord and tenant.
There is pretty much nothing that will work as far as I can see. Why not just make hardcoded relations that make sense and not do half assed incest like this? Hardcode it as a close family friend taking her in and write the script around that.
Lisa referring to her aunt and uncle by their names is not a problem, just as it's no problem for her to refer to family friends by their names, whether they took her in or not. Sure, in some cultures, she would have to call them "Aunt X" and "Uncle Y", but in modern Western cultures, that isn't really a sticking point, especially when Sharon and Touma have given her a somewhat unorthodox upbringing.
As for the user defined relations system being bugged, the only instances of that which we've encountered so far are cases of Lisa calling Sharon "Mom", no matter how you've defined their relationship. These early goofs have, I believe, been corrected now. Apart from "landlord/landlady" references, which I would like to see purged from the game, there really isn't any problem with the user defined relations system.
As for why the developer went this route, instead of hardcoding relations, I think that should be obvious. It's because of Patreon and their censorship. In my opinion, all adult game developers should say "Fuck Patreon" from the beginning, and use other options for funding. But people sometimes insist on shooting themselves in their feet.