I think it depends ( or at least I hope at the very least) on the manner of which the mod is changing the relationships. And also if the Developer endorses or supports the mod. Pointing people to it. Making it seem like they could be working together with the mod creator.. silly but .. it's Patreon.
If the patch is merely a simple variable switch and the name changes are already in the game just disabled then Patreon will probably take issue. Also maybe if they deep dive and the variable names are MOM or SISTER.
If the mod changes the names specifically, altering dialogue to fit with incest then I would hope Patreon realizes that is outside the control of the Developer.
I also hope they have no problem with being able to define the relationships via inputting during the beginning manually with default being the silly Landlord.
I'm probably giving Patreon too much credit tho
I feel like a new stance on Patreon's side is they just flat out removing the games, only saw them being put under review before. But maybe that is just for the more popular games with higher sub counts like Lewdlab etc.
EDIT: Just looked at this incest patch and it fits within what I thought would be acceptable...