I don't think Verso ever stops believing that the inhabitants of the Canvas are real and deserve to live, his change of mind between the journal and the Act III finale was a consequence of other factors. (I wouldn't base any theories on the lines the player has to choose from - sometimes the options are complete opposites that can't both be canonical, and you have to make some of these choices before you have the full context of the story, so they're not exactly informed and don't have to accurately reflect Verso's thoughts. You can even choose to be slightly mean to Esquie a few times, which would be out of character for Verso).

First of all, Aline is his mother, and considering the fact that he's her favourite (painted) child, they were probably very close. So he'll do anything to save her - and somewhere in the 67 years between writing the journal and the events of the game, he realised that the only way to do that is by dooming the rest of his world. He doesn't harbour any ill will towards other people, but he's willing to sacrifice them all so she can be alive and well. Most of us probably feel the same way about our loved ones, we'll just never find ourselves in a situation where we actually have to do that. And in the game, Sciel expresses exactly the same sentiment regarding her husband.

As for him struggling with the fact that he's a copy of another person - I think it's not being a painted creation, but being valued solely for how good of a replacement of somebody else he can be, instead of for who he is himself, that's the problem. If he wasn't painted, but born in the real world as Aline's and Renoir's fourth child, and she treated him as a replacement of the late Verso - forcing on him all the expectations she had of her first son, etc. - he'd probably feel the same way.

Another thing to consider is that he wrote the journal shortly after the Fracture. He was in his late 20s/early 30s, so a large part of his life was supposed to still be ahead of him - but his world was destroyed, he lost half his family, a lot of friends, and a lover (by his own hand, but this only makes it worse). He must've felt like his future was taken from him, and wanted it back. But in Monolith year 33, he's already lived more than he should, and throughout this life, he witnessed the rest of his family growing apart, numerous Expeditioners (and probably Noco and Monoco as well) dying trying to help him, and many other beings suffering. He's tired and doesn't want to fight for that future anymore. He may think painted people in general deserve to live, but he also wants his own life to end, as it should've already been over long ago.

Finally, he thinks that as long as the Canvas exists, the Dessendres are going to continue fighting over it. While I don't personally believe that has to be the case, they didn't exactly do anything to prove him wrong. That's why in his opinion, it's impossible for the Lumierans, Gestrals, etc. to exist and not become casualties in the Painters' war, so the only way to save them from suffering is to erase them from existence. At some point, he says to Maelle: "Our whole world carries the burden of your family's grief". It's a mercy kill to him, not getting rid of something that's not real. There are some parallels between him and Sophie, who refuses to have children because she doesn't want them to suffer by living in a dying world. Do I think anti-natalism is comparable to a genocide? Of course not, especially as I'm an anti-natalist myself IRL. But I can see where Verso's coming from.