So I have a big theory and I don't know where to put it, so here it goes:
The thing that's gonna incarnate in Yuri's stomach isn't Aono. Is the patron god of the village, Kubinashi sama. The dark Aono is the real Aono.
Based on the whole thing with Sota and the school inventory, we know the ghost always come back, because you're not supposed to offer them anything, and as soon as you do they're turned into evil spirits. We also know from the Sota situation, that every time someone comes back, a part of the patron god, with them. In Sota's case, his "friend". The part where Aono says that it isn't Yotsukubi sama, nor a ghost, but at the same it is, shows that the existence of Kubinashi is not something that's fixed. Furthermore, my theory is that Kubinashi sama is feigning being Aono (the "good" one) due to Yuri's agreement.
Think about it. Yuri and Aono were only dating for two weeks, yet Aono seems to be the perfect boyfriend, despite Fujimoto knowing that he only dated Yuri because he felt bad for her, and that he didn't really knew her. My theory is that this Aono is the part of the agreement of Kubinashi with Yuri: it gave her her perfect vision of Aono, so that she would be satisfied with it and never taking back her agreement. This is why this Aono doesn't have complete memories of how he died, or his childhood. Is an incomplete version of Aono. This Aono also evolves with the time. Every time Yuri changes, Aono also changes to satisfy her desires. This is why the normal Aono didn't know about what happened in the aquarium, but as soon as Yuri learned about it, he suddenly was able to.
Dark Aono is the real Aono, which is why he only comes when certain steps are taken. As the boyfriend of Yuri he doesn't want to hurt her and he is technically part of the deal with Kubinashi. Similar to Sota, who is part of the deal, and is seemingly the perfect brother, that is also part of the deal; Kubinashi only brings back the parts of the deceased the one making the contract remembers. The "dark versions" that appear are the real ones that have grudges and can't pass on. This also explains why he wanted her to eat food of the other world, that way if she gets stuck there, her agreement with Kubinashi will be void.
Dark Sota holds a grudge to his mother for "forgetting him", and to his brother for "causing his death". Dark Aono does not hold a grudge to Yuri, but as a dark spirit, both of them have the desire to grow stronger by getting offerings and sacrifices. The reasoning of this is that those things are different; offerings are usually made directly to the deceased, normally on their tombstones or the family altars, sacrifices are made to deities, and can be done anywhere. So far all the offerings have been made directly to Aono (the food, the eyes) which is why only the dark Aono, the real Aono takes them. The normal Aono can't take them, cause he's not real one, thus they aren't his to take. This explains why the normal Aono couldn't enter the storage room, but dark Aono could. This also gives a possibility: normal Aono can't afford to let Yuri know that he's not the real Aono, cause otherwise that would void the agreement. In agreements, the spirit cannot lie, but they can hide things. This is also shown on the agreement to bring back Sota, Hiroto wasn't told that he was gonna come back as an evil spirit. In the same, Yuri wasn't told that Aono was gonna come back as Dark Aono, and to make her less suspicious, Kubinashi decided to disguise itself as the perfect Aono. If Kubinashi has control over all the spirits in the village, then he could keep dark Aono at bay, except when Aono is called directly, cause that's part of the rules. That's also why normal Aono remembers everything Dark Aono does, cause technically, spirits are part of Kubinashi's domain; not enough to control what they do, but enough to know what they do.
So, Yuri sacrificed herself, offered her life in exchange of Aono. Now based on the Kubinashi ritual, we know that every ghost agreement isn't made with the ghosts, but with Kubinashi sama; the ghosts are only part of the exchange. And Kubinashi sama makes use of the sacrifices however they seem fit or convenient. In the kids case it involved a game, but in Yuri's case it involved being reincarnated. We also know ghosts can't really come back, except as well.. ghosts. So that further solidifies that argument.
Part of this theory is that Nozomi's family is a family of ommyoujis. But that due to the times changing, and the lack of sacrifices, they probably left that tradition behind, and thus Nozomi was never really talked about her heritage. This part comes from the fact that Nozomi's grandma seems to know a lot about the village story with Kubinashi, and despite being a ghost she has powers that ghosts otherwise don't have, like taking over Nozomi without her permission, entering her dream, or taking control of the snake in Nozomi's dream. This also comes from her clothing, which are clothes people wear to funerals (the visitors are the ones that wear it, the deceased usually wears white clothes), but black clothes are also associated with the highest rank of Shinto priests.
Furthermore, Nozomi's grandma is effectively Nozomi's shikigami as of now, one out of devotion and not sacrifice. This is why she helping her during her dream was accepted, she is technically an extension of Nozomi.
Another part of why the agreement with Yuri is different, is because they're kids. Yuri is a virgin who's in age of conceiving (the chapter showing her having her period wasn't a coincidence). Ghosts cannot come back, but deities can, given they have a vessel. In this case, Yuri's stomach. The fact that Yuri's family has a history with Kubinashi isn't out of the question, neither. It's is possible that like Nozomi's family, Yuri's family must have a tie to the Kubinashi ritual in some way. If the Kariya family has a tie to sacrifices, it could even possibly explain what happened to Yuri's older brother. Let's not forget that in some traditions you're supposed to sacrifice your first born. This could also explain the situation behind her older brother.
Now I know this is wild but, my theory is that Yuri's parents had to sacrifice his older child, and had Midori hoping she could be sacrifices instead. As per the rules, only the first child was accepted, and they grow to hate Midori because of this. They had Yuri either as an unplanned pregnancy, or in hopes of having a second boy to replace the first one, but it failed. This is also why the first child is never really talked about.
So, not only the Kariya family has something to do with sacrifices, and abnormal virgin pregnancies related to deities; Yuri would inherently be sacrificing her first born by making her birth a god.
So, the theory is this: the village where Yuri lives is controlled by Kubinashi, and her family has a tie to it by doing sacrifices, and Nozomi's family by being priests. Yuri didn't make an agreement with Aono, she made an agreement with Kubinashi to bring back Aono, and now she has to birth Kubinashi, while Aono returned as just a dark spirit.
