How can the mangaka justify this as legal even in an imaginary universe?

I mean they used a “live body” to make him and a child at that.

If we are talking about legal things... more than half of the yaoi mangas would be illegal work.
Have you heard about Boku No Pico?

Boku no piku is just plain weird. No connection to reality whatsoever whereas this is trying to be realistic. (A slightly alternate reality but still...)

I guess it just hit a bit too close for my taste and what probably really got to me was the indifferent reactions. Like it was completely natural.

I have read plenty of yaoi rape and this includes the mangas where it was actually painted as rape and not romantic coercion. Of these at most four actually made me feel sick to my stomach. Sure I’ve felt for the characters in other yaoi mangas but the reactions of the characters felt so far removed from reality that it still felt completely fictional.

Sorry... I guess that got a bit darker than I intended initially (￣∇￣")
(Feel free to ignore my rambling)

No the author doesn’t justify it is the problem. It’s the reaction of the side characters that says it all. There is not a shred of remorse or any real emotion attached to this whole scenario. It’s like it’s completely out in the open though not well known. It doesn’t seem like it’s covered up at all. Sure our protagonist does find it wrong and I’m guessing that that’s the general consensus among ordinary people. But this whole thing does not seem to be illegal in this universe. It’s like some unethical science experiment to further rich peoples wealth that everyone in the general populace finds disgusting but does nothing about because ‘that’s just how it is’. I don’t know where I’m going with this... It just irks me.

That got long... not angry or anything but I can’t really figure out what my actual problem is and usually when something irks me I know what it is...

Well every mangaka tries its best for their manga to create some kind of universe within their story otherwise it would be lacking, and obviously we encounter the predicament of moral and ethic in this being with using humans as sexual bots and kids at that. But the fact that he/she managed to confuse you and somehow bring disgust towards the immoral characters just proved that she wrote and draw her story well.

you already said its an imaginary universe, the author did nothing wrong, it's you that's wrong...

Well that's the whole point of introducing Shindo's perspective, to question the morality of the universe.