The issue with this is that though shrines can change hands in ownership, they only belong to one god. For example, moriya has kanako, myouren technically has bishamonten due to shou, and hakurei we don’t know. Reimu’s god channeling is similar to yorihime, just not as “at will” as yori. The shrine in general seems to not have any people worshipping for one specific thing, which is why it’s so hard to pinpoint the god.
So you're saying even my joke Yorigami sisters theory is more likely? lol. But good point in debunking it since where here to discuss and try to figure this out.
Looking at the lore, I think the character who most fits the role of the Kami is Yukari. She is clearly a woman of immense power (I mean she is so strong she enslaved a powerful yokai as her minion, who in turn enslaved another yokai). She is repeatedly at the center of Gensokyo's formation and history prior to Reimu's rise to power, and has a vested interest in Reimu's success and power. She also is very protective of Gensokyo. If my memory serves, she imposed the Spell Card rules after Remilia's arrival. She also banned eating human flesh, and humbled the youkai in a pointless war when they had plans to spread outside Gensokyo. It also fits the implication she is a human who became a youkai. If she could grow from a human to a youkai, why not a youkai to a kami? Humans have become both in Shinto after all, and her deeds would qualify her for the rank of Kami...that is, if anyone worshipped her.
I gave this some thought and came up with something to add on: Rather than Yukari being the Kami, I believe that Genoskyo itself is the Kami. Yukari, then, I believe would be the physical manifestation of Gensokyo. But if everyone knew Yukari is Gensokyo and its kami, that may attract more unwanted attention and deter her from protecting it. But if she's just a "very powerful Youkai" then she is, at the end of the day "still only a youkai" and merely feared.
So through Reimu's actions is how she 'gathers the faith" in a more roundabout way. The Shrine itself would be her true base and the "poverty" of the shrine would be intentional to keep the excessively curious from figuring this out.
I'd say even Reimu doesn't know and that too is part of Yukari's plot. Reimu would be too obsessed with wanting to relax, getting donations, etc. rather than trying to ever genuinely sit down and think about where her powers come from. Her personality happens to be the ideal type for Yukari to manipulate, which is probably why she was chosen (something I don't recall ever being shown/mentioned: How Hakurei shrine maidens are chosen. Even if one argues "bloodline" then who chose the very first Maiden? Reimu clearly isn't the first one...)
Someone brought to my attention recently that many outsiders who come into Gensokyo tend to first appear at the Hakurei Shrine, as if the shrine itself is a "gap" or rather, that it is the borderline between Gensokyo and the Outside World, as in, it is the only place that overlaps the two, but only Yukari is able to fluidly go between them.
So then, perhaps the Torii itself of the Hakurei Shrine is the final border between the 'mundane' (outside world) and the sacred (or 'fantasy' in this case: Gensokyo) and the moment one walks into Hakurei Shrine, they are in a unique place in Gensokyo that is "closest to the outside world" but still not quite there. Taking this into account, no one would ever think that gate is "reversed" as the Hakurei Shrine is the
least sacred area in Gensokyo as it is the 'closest to the outside world" Once you step outside the shrine and into the rest of Gensokyo, is where the 'sacred fantasy' begins. Even if this is isn't completely accurate in terms of how Shinto Shrines work, Hakurei Shrine is no ordinary Shrine to begin with and therefore I believe some exceptions could in fact be accurate.
I hold an additional theory that Yukari keeps everyone imprisoned within Gensokyo and thus why no one can leave it unless she allows it. After all, no matter how powerful you are, if no one believes in you, you're no 'kami'. If people started leaving Gensokyo and if Yukari is indeed the Kami of Gensokyo as a whole/Gensokyo itself, then she would lose faith/followers/power if people started leaving.
Going back to Gensokyo=Kami: Both us in the outside world and the residents of Gensokyo who believe in Reimu's power to resolve incidents and protect Gensokyo are where the faith comes from and thus why, give or take, "Reimu always wins when it matters" despite clearly not being the single most powerful being within Gensokyo.
Lastly if Genso=Kami=Yukari, she may actually "nerf' Reimu to only be able to utilize her full power when needed, both to hide her true identity as a kami and the physical strain it would cause Reimu as she is, at the end of the day, still human.