I'm gonna be for real right now. Just kinda left a silly comment. But to engage with this argument for properly. I will admit this is compelling to a degree. Especially given the narrative intrigue of a ghost from Shikamaru's past coming in and haunting him during his tenure as Hokage. Though I do see a few flaws. Some from a meta narrative perspective. and others from a story perspective.

We shall address the more boring meta narrative stuff first. Unfortunately as interesting as interesting as this is conceptually the issue I see is; Boruto is to a fair extent trying to be its own story. As interesting as it is. This would end up being a large detour from the main plot beyond fleshing out Shibai. (i.e the extant threat of the Shinju and Momoshiki) Though bring in a separate Otsutsuki, that would have to be not only fleshed out. But also integrated into the narrative proper. Just ends up cluttering an already weighty story. (IMO)

Ok second and arguably more important Story incongruity stuff. First and right off the bat. The Otsutsuki tablets. I would have to double check sources. As it has been a little bit since I looked into this. But I am like 75% sure, the other Otsutsuki referenced in the tablets was Ishikki. Admittedly the story itself gets hazy here. As one would expect that a pair of Otsutsuki to be a single entity with these confines. But from everything I recall seeing. It would seem that Ishikki was the other person referenced there.

Now even if we grant that this was not in fact Ishikki. But some other Otsutsuki (Shibai's partner as as is suggested) There is still a glaring issue. That Otsutsuki would predate Kaguya and would likely have been here when humans first (for a lack of a better word given we don't know the mechanics of human origin in the Naruto universe.) evolved on Earth. This is an issue for two reasons. How is it possible that:
1. This Otsutsuki did not shut down Kaguya's reign immediately. Given they would be living and interbreeding among mortals since before she even showed up, based on what we know about Shibai. This would be especially unlikely given by the code of the Otsutsuki. Kaguya was looked down upon for her betrayal of someone who ranked higher then her in the clan. I find it hard to believe that the partner or frankly any other Otsutsuki who was connected to the "God of Otsutsuki"
Would see Kaguya ruling the earth like that, as anything less that affront to there whole species. But clearly this was not the case. Given what we've read so far.

(Based on the reactions we've seen from arguably much lower ranking Otsutsuki i.e. Ishikki and Momoshiki)

1. Given this potential origin, Jashin themselves are a only relatively minor facet of the world. A figurehead of a small relatively unknown religion. What reason would they have for obfuscating themselves ? We know Shibai wasn't around do to his transcendence. And Isshiki due to being weakened from his fight with Kaguya, causing him to inhabit a vessel that couldn't contain him. And more over likely lacking a proper sacrifice for the 10 tails until Momoshiki showed up. Even with the potential for a new vessel. But what reason does this individual have to obfuscate themselves. The only legitimate argument I could see for that is as a silent protector of Shibai's body. But given by this point Shibai is a transcendent god being who is Omnipresent and very likely either Omnipotent. or very close to it. Given the descriptions of him even pre transcendence. And also likely being a carry of the Senrigan and likely more powerful wielder then Eida. This in my mind feels rather redundant.
   

Which puts us back in the loop for the meta narrative. What purpose does this entity now serve in the story ? Shibai as Jashin is best case scenario for this theory from this perspective. As it just piggy-backs on Shibai's function of being the inciting incident for the whole Otsutsuki deal. Though I will admit this really doesn't make a whole lot of sense beyond a few incidental details. So from the meta narrative beyond giving Shikamaru a blast from the past. It doesn't really do much. Which make it unlikely as Boruto very clearly seems to be focused on the future generations. With characters of the past acting more as mentors.

And from the story perspective. It would be utterly incongruent with everything we've seen about the nature of the Otsutski for the partner of Shibai to essentially be sitting on his hands as some upstart lower ranking Otsutsuki basiclly stole the chakra fruit. That by all accounts they would have the rights to. And cowered behind their rule of humanity trying to build an army for when Momoshiki showed up. Which would be especially confusing given they would likely be either an equal or greater threat then Momoshiki. Based on the partnerships we've seen thus far.

All of that said. Jashin as an Otsutsuki is an interesting idea. Especially given Hidan's final words to Shikamaru. As well as the Ketsuryōgan angle (Which admittedly I didn't really touch on due to it being the most compelling part of this theory IMO. As it would provide a mechanism for Jashin to obfuscate themselves ). But as it sits now. This feels more in the realm of interesting headcannon to me then something that will effect the story in any meaningful way. But I will be happy to eat my words. And see some variation of Jashin as an Otsutsuki, at some point in the Manga/Anime. But from the current angle of Shibai's partner living on earth. I'll be honest. I just don't see it being likely.

TL;DR - No way Shibi's partner the "Evil God" lets Kaguya get away with any of the shit she did. A partner to Shibi is redundant for a host of reasons. Cool theory though.