you assume the Missing Posters are mostly right, and you all are caught in the STEM from before the beginning of the game.
Obviously there's several problems with this (most notably Dr. Marcelo Jimenez's character and the outro), but bear with me.
1. Young Ruvik is supplied with materials, victims/subjects, and coverups through Mobius, the mysterious organization that Kidman and Jimenez both work for to varying degrees.
Now, Ruvik appears to be at least somewhat ignorant of the extent of all this, but it makes much more sense than pinning all of the disappearances and the like on him solely. I mean, we already know that Jimenez and the Beacon Hospital staff are funneling him people and helping cover for him some, and it's also established that there are.... oddities at Beacon (and its ownership) that probably can't be laid entirely at Ruvik's feet. The Newspapers go over that.
In addition, how superhuman do you *really* think Ruvik can possibly be in the real world? Now it's good odds that not all of the Haunted and their ilk are one-to-one people.... while we have definite evidence that some of them are, and that Ruvik has fed *many* victims into his psychoplane (more on that later), you end up killing and evading hundreds of these guys.
Most likely several of these are copies, figments, personifications. I mean the Keeper is almost assuredly one, as well as Faux Laura, the Church Dog, and some others that are more obvious than others. The model files you unlock after completing the game seem to agree with this assessment.
We shouldn't downplay that, yeah, Ruvik murdered a LOT of people. But we are in a madman's world, and that should be noted.
2. I'm going to take a moment to address an important and flawed aside with the entire fucking game: the church cult.
I'm reasonably certain that this is a part of the game that got partially cut. This is a big section of the psychoplane, but we have little to no reason to think that Ruvik had anything to do with this in life.... at first I thought that maybe he spent time with them in-between his time at the manor house and ranging abroad, but none of the documentation you discover supports this, none of the research the cult was doing is in line with his, Ruvik is *far* too solitary a man to be involved in a group effort like theirs, and the model files themselves seem to indicate that the Church section is an anomaly.
The strongest connections between Ruvik's scheme and the Cult are the following:
1. Both were doing violent, murderous mad science.
2. Both were operating in the region surrounding Krimson City
3. Both appear to have had access to supplies that were beyond them
4. Fernando Cabrera
Cabrera is referenced in both the Missing posters and the Newspapers, as speaking out about the cult and as being a long-time Beacon inmate.
It is my strong suspicion that the Church region of the psychoplane was originally designed with Cabrera as a focal point, possibly a particularly strong/durable madman fed into Ruvik's brain-hell that was managing to hold on and twist the surrounds to his own self, along with other possible cult members that were incidentally captured by / given to Ruvik.
Remember, Jimenez remarks that the world is not entirely at Ruvik's discernment; *all* of the minds trapped in it contribute to it. There are several sections of the game that Ruvik probably didn't have access to in life, or were built whole-cloth from ideas, or were drawn out of other people's minds (portions of Beacon, very possibly the Hospice, etc.). And we've already seen that people can hang on for indeterminate amounts of time before giving in and being devoured by the madhouse. Sebastian, Joseph, all the others you interact with, the guy near the beginning that 'can't hold on' and transforms in front of your eyes, the woman thrown on the pyre and the man beheaded in the guillotine are all people who've held out, for a while at any rate. The written scraps you find here and there seem to back this up (like the early one near the lake that implies confusion about the geography and time).
Anyway, while there is too much Church-region stuff to be solely from Cabrera's mind, I think he's a plot thread / miniboss they dropped before final production, but went ahead and kept a bunch of already-finished things in from. It pads the game, increases the murkiness of the waters, and gives in to Mikami's known fascination with religious-based mad science cult themes. I'd argue that the game implies that Mobius had a hand in the cult as well, and possibly fed some of them to Ruvik anyway.