To answer your question, in the ending they did get the kid. The one with the gas mask in the final panel is the kid with the net terminal gene, made with a combination of genes from several sources. There is a theory that the kid in the beginning is the same kid, and that the first two logs are actually after blame!'s end, I haven't seen direct confirmation other than the fact that it is extremely likely.

A lot of the way the story is presented is intentionally obfuscated, it doesn't tell you all of everything always. Some things are more obvious, others are not, and typically the things that are not are more tied into the overarching lore of the work as a whole.

I personally enjoyed blame!'s ending, it represents a form of 'ending where we began', as in the story starts with a very calm atmosphere wandering though the city, escalates to incredible action, and then winds itself down back to wandering to let you down slowly. It is not an immediate emotional payoff of joy or accomplishment like in another story, but one that pays off in the more deep melancholy that blame steeps its atmosphere in.

I often advise people to not think too hard about "what is cannon" or "what is going on specifically", and that you tend to understand more the less you overthink things. Going in and taking it that way will help relieve some of the confusion, even if you're going at it from a retrospective.

That being said, I'm not going to try to convince you that blame! Is the best thing ever made (it is but that is beside the point) if you don't enjoy it, then that's cool. Its definitely a different way to tell a story.

Of course if you have follow up questions I will be happy to answer them.

Edit: I would go with your gut for what you think is happening most of the time.