I wasn't happy with his evolution being called artificial either so I just headcanoned it as our arbiter using the material available to facilitate it, rather than us just haphazardly evolving, similar to what you're thinking. I'll similarly be annoyed a bit if the mc ever ends up using one of those serums, it just feels like those serums don't evolve you in a way that conforms with the apostles/arbiters plans because you take the challenge and ordeal out of the equation. Mostly pure headcanon on my part but will be interesting to see what's actually going to be happening nonetheless.I didn't call MC's evolution artificial, Xanthe did. That's why I put "artificially" because that's what Xanthe believes.
For me personally, I think the MC evolved naturally and the reason why is because of the Origin itself. I'm of the belief that the Origin used the surrounding monster energy to wake up fully and pulled the MC to his realm. After they had their little talk, he triggered the evolution itself for the MC. We already know he has the power to push him beyond Level 5 by being reborn, so a jump to level 3 from level 2 seems like minuscule task by him in comparison.
Only problem with my thoughts here is the different lingering monster energy that remained inside of the MC. It was still left over after he evolved so that puts a hole im my conclusion. Maybe it was used as a cover but meh. It most likely was just the monster material that triggered it and I'm just thinking of any reason for my MC to still be a purist with Evolution.