That's all very interesting Qolem, especially the bit about how the MC bribes others for information on ninja with the intention of making different phantoms. BUT that being said I find 2 issues with your theory.
1: Only Scarlet Blaze is stated to utilize Genjutsu. And if it was genjutsu then it would be fitting if his illusions were listed as "Phantom " just like the Hokage Brothers genjutsu from the "Maiden's Genjutsu" instance in Chapter 4.
2: The game explicitly states these are "clones" when you use your fragments to add a new ninja to your roster. It doesn't tell you what kind of clone, but they are superior in quality compared to all forms of the technique that we're aware of, making it most comparable to White Zetsu's ability to masquerade as others. These clones have green health bars, so they're not treated like typical summons that disperse upon the summoner's downfall. They also need to be cultivated & strengthened, a way of symbolizing your character's growing knowledge on the person, their style, and how they believe they could be improved. And most importantly not only can they grow, but they c*so reveal the potential of the original! 1* Sakura is the only example I've found, but she has the ability to heal others when it took the real Sakura 3 years of training under Tsunade to develop her chakra control to that extent. But if you notice 1 & 2* Naruto, they're ability to generate clones is at a much lower frequency when compared to the original when you fight alongside or against him. Which makes sense when you think about it since it had been mentioned that creating clones divides up the user's chakra, and making too many clones could be dangerous. So the more comfortable & experienced the MC is with Naruto's Multi-Shadow clone jutsu, the better he can replicate those effects later on.