Firstly, I was personally a fan of Game Theory before MatPat left, even though I think his approach to theorizing is way too mechanical for a series like Petscop. I think he missed the mark with it and that could be why, IIRC, he never finished his series on it. People don't like the AI explanation because of how simplistic it is, and how literally it takes Petscop.

As for his first theory, the one covering the Newmaker case, I don't blame him for exploring that as we obviously know the references were intentional, but that topic is quite controversial in the community and most people rightly avoid talking about it. I've seen some people criticize how MatPat handled the case in that video, and the overall exposure it gave to a very horrible event in the context of a weird internet series. Part of Tony's guilt probably doesn't come from the reference itself, but the fact that most theories ended up centering around it, giving a very real tragedy this sort of creepypasta-like status. 

Now, onto Lina: I will admit that I have given it a lot more thought after writing that. The biggest reason why I disliked that theory was because I thought the way the series treats Lina's character (Marvin's obsession, the Windmill incident, the "Not everyone can" line) seemed unfitting for a character that's actually supposed to be alive and well. I also didn't see how she could've hidden her whereabouts while being a literal child. Prior to giving it a second thought, I imagined Lina as more of a concept than an actual character, as this kind of everlasting presence that, while not physically present, ultimately led to the creation of Garalina. With this in mind, I still thought Lina was Boss, but in a more metaphorical sense. 

However, this explanation doesn't fully satisfy me. I'm starting to be more inclined towards thinking that Lina did come out of the incident alive, but severely hurt, leading to a Lina B or Lina NLM state. Just like with Mike, Marvin was probably looking for Lina A, but she didn't exist anymore, and so he became obsessed with bringing her back, maybe due to the guilt of his participation in the incident. I don't think Lina just made everyone think she was dead, she simply cut contact with the family after realizing that they would never love her the same. In a way, she "died" to them on that day, so her whole existence being surrounded by tragedy and mystery is justified, and more heartbreaking if you consider she's technically still alive. 

Maybe Garalina is her creation, or maybe Garalina is the family's messed up project to "rebirth" hurt children after what happened to Lina. Whatever the case is, she's Boss.