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The sister imperator comics deal heavily with abuse. Sister's step father rapes her off screen (and murders her young sisters), and this culminates with the depiction of her self-induced abortion via crochet hook. [imgs from this post]

in later parts of the comic (cityofmeliora has all issues posted here), Marika meets with Sister, and insists on adopting her in their family. While this is not shown to be an official/legal adoption, her time with the Celeste Circus is heavily emphasized by her accepting them as her family-- especially Nihil and Marika as her siblings. Here is where we actually see her accept her new name as "Sister." I would link more panels here, but this is basically the entire plot of the comic. It's about Sister determining who her family is, and her devotion to that family.

Due to Sister explicitly entering a sexual relationship with her adoptive brother, this is incestuous, but not consanguineous (we do not see this type of incest depicted anywhere in Ghost lore).

There are also panels where the art heavily suggest attraction between Sister and Marika, and Marika and Nihil.

The comics set a standard for the blurred boundaries between family members within the Ghost universe. The give and take between the condemnation of it varies on whether or not it's happening on our protagonist's, Sister's, own terms. Sister is a survivor of abuse, but she is also a villain in her own right. My own takeaway from this depiction this that abuse often perpetuates more abuse. Ghost in general covers the cyclical nature of the horrors of our world, and the depiction of this type of violence is simply one aspect of it.

Chapter 23 had Sister's ghost behaving odd and flirtatious toward Cardi, and the more bullshit I see about boymoms and how new age religions maintain control, I don't think this is out of character.

As for PapaxPapa, Nihil and Cardi are really the only two Papas we've seen with any meaningful interactions (in my opinion at least). I can't really make a case for anything too disturbing happening between them-- aside from Cardi's weird ad-libs about him that are a bit awkward.

I think for the most part, people ship PapaxPapa because they like yaoi and it's not much deeper than that.