In all fairness, if the "early version" is nothing like the final product and would grant the game a "R18" mature label...Sega wouldn't allow that for pretty fair reasons.
1. Limited Audience - Sega managed to market Sonic and his games to a wide range of people across the world. So, to imagine them taking inspiration from Outlast, Saw and Manhunt (one of which actually being banned in Australia last I read) is...unhinged and unnecessary. If they have a good thing going, why tamper with their usual workflow for the sake of being edgy? Shadow the Hedgehog filled that slot just fine and that was relatively handled well enough since he essentially has his own community of fans himself.
2. Limited Money - Short but simple: Sega would lose their financial status if they tipped into this section out of the blue for no reason. You can't exactly say "The Murder of Sonic" could involve random graphic scenes of torture/violence, potential sexual violence as well as hints of other 18+ related material and market that to 13 year olds or older. They would lose a significant amount of money if they released such a graphic copy of this game to a random gaming platform.
3. Lawsuits Incoming - As mentioned in both points before, Sonic is often enjoyed by people with a variety of games. But, most games are seemingly marketed for both children and adults to enjoy. Seeing basically Outlast, Saw and Manhunt being used in this "totally legit copy" would likely cause whoever made it to suffer lawsuit after lawsuit given the fact that would essentially be plagiarism (if the creator tried to take full ownership of the game, contents and all).
Not only this but Sega essentially would be tagged about the creation at some stage, check out the game itself and likely strike the creator with a cease and desist for trying to ruin their mascot's reputation (similar to the SML lawsuit with Nintendo).
The "bootleg" seems more like a reason to hype up gore and/or graphic scenes in general rather than be an established Creepypasta. I mean...come on, it's Sonic the Hedgehog. I get that Shadow has a gun, Maria was killed as a child and some characters do have pretty striking deaths but referring to Outlast for this game? It's a bit excessive, even for Sega.