both count as incest. as does stepcest. although if the sisters don't actually do stuff to each other during the threesome you might get away with it.
there are several ways you can go about it, which depend a lot from that 'relevant part of the story'.
for most trivial cases you can just change a couple of variables and restrict the 'incest' to those only. change 'sister' to 'friend' or something like that. works pretty well when there's no actual story. this can be done in a patch or by asking the player to define the relationships at the beginning. the problem with latter is the player won't know how exactly YOU used the variables so there might be misunderstanding. also it'll be problematic for writing incestuous hot dialog during sex. I mean you can't make them say: "fuck me, I want to feel my FRIEND's cock deep in his FRIEND's pussy!" so you avoid lines like that during writing. basically it only fully works when they don't show any incestuous behaviour towards each other. which kinda defeats the point of making it incest in the first place.
but when you have essential related story you quickly get into more complex problems than just changing names, like how do you explain the flashback to childhood where you live in the same house with your 'friend'. you might find out you need to write two versions for the critical parts, incest and noncest, then have a boolean to switch between them. so the patch only needs to change that one variable, and you've already done all the real work under the hood. the good thing about it is the versions don't have to be identical, you can have different flashback for both of them. maybe your sister grew up in your house, but for your 'friend' the flashback happens in a completely different setting. you don't have to do that, but it's a good option if you have a scene so crucial you just can't make it work for both cases with text changes only.
the most laborous (for the modder) is to externalize all the incest dialog into a '3rd party' patch, which will then need to be remade with every new update. the upside is NO incest is present in your code, but it's laborous and if the patch is not made by you the added text might be anything. some people are paranoid about patreon looking inside you code and seeing the incest dialog, but I highly doubt the can be arsed to do that.
one thing about patching is it can't be connected to you, even if it's on another site outside patreon. in the early days some were burned by that. I can't remember it happening after the beginning, but that's still possible. so the patch needs to come from someone else, or 'someone else'.
in the end though none of these are foolproof, there's no laws forcing patreon to be in any way consistent about it. even if there were not a single bit of incest present, they can boot you off one day just because they don't like the smell of it. which also means that anything they now say is fine might one day be not.
the reality though is they seem to only act based on complaints, and several of the biggest games have bannable content right there in the open. and for what I've seen they've been very cooperative about the changes they've required for unbanning. in my opinion it seems they're only acting when forced to, so they can say they're taking it seriously. but of course they know what every game with 'landlady' and 'roommates' is really about.
those are the main things to think about.
