Spoiler for NoWaYu and KuMeYu spoilers inside:
It looks more and more like Yuuki Yuuna is a arahitogami as was surmised at the end of Season 1. Its just that now it seems she did not come out of nowhere but is the reincarnation of Takashima Yuuna It might even be better to say that Takashima Yuuna was the one who originally became a god.
Yuuna being a god and becoming aware of it before she gets herself killed or loses her mind is important. Because she would be the only god on humanities side who is not fixed in place as part of Shinju, and she can do things like protect a new tree created by the seeds mentioned in Sonoko After and KuMeYU. This would break the deadlock as humans could now act without weakening Shinju.
If the above is true then it makes sense that Yuuna would be able to "feel" Tougo in danger even with Shinju's memory erasure. If Tougo really is not just a Miko but Yuuna's Miko or even priestess, they have a connection that they cant break even if they wanted to, and will continue even when Yuuna's human body expires. And after today and that brand thing appearing on her chest, that looks like its going to happen sooner rather than later.
When Yuuna said she "remembered this place" was that from when she was in a coma- or from when she, as Takashima, was absorbed by Shinju to keep her from dying thus allowing Shinju to return her later? Gin proved that Shinju does not contain the goddess of the underworld and cannot return the dead to life. So when Takashima was wounded and about to die, Shinju grabbed her. This may not be the first time she has been back either, given the hints in KuMeYu about an earlier war inside Shikoku with Vertex worshipping cultists. Japanese theory on arahitogami goes that just being born, sent from heaven is not enough, arahitogami also require events to occur during their natural human lives to challenge them and allow them to realize their godhood.
Having a God that had lived as a human on their side also could stop this chronically bad communication between humans and Shinju, and for that matter the attacking gods as well. This again requires Yuuna and Tougou to fix their OWN bad communication first.
I must admit I am biased. My perfect ending is for Yuna to be confirmed as Yuuna no Kami, cause Tougou to give birth to a demi-god daughter that Tougou and Sonoko would raise and name Gin. This girl would then become a Yuusha in turn, defeat the heavenly gods, subjugate the Taisha and be proclaimed Empress starting a new dynasty.
This is my Togou-esque rant for the day
Do the writers have the balls to do this though? Probably not. Although if they did we would be in Yuuki Yuuna stories for a decade or so.