In chapter 4 it npc said that the mutations started a few years ago meaning that Mr A couldn't have given birth to him because no way Little A is anything younger than 16 (not that they would write an underaged character)
And the foster parents thing can easily be disproven by the fact that Mama A looks like both Mr A and Little A.
As for the box, I have no idea
But one thing for sure is that Little A doesn't have all of his memories. With him not remembering the "incident" as well as him not being able to remember fluffy who he is seen playing with back from when he was a doggo.
Nah you good I think another theory I had which is darker than I originally thought but maybe what was in the box was pornographic images of hybrids breeding with one another and that’s where I think Little A gets his fetish from because homie be way into doing the hybrids that or it could be his animalistic characteristics but that was my other theory

…….
Ok so this is my theory so I believe that Mr.A was affected by this mutation and gave birth to Little A, maybe the organization took him with false parents or Mr.A couldn’t raise him. However I think the day he went to look in the box is when he found pictures of the day he was born and saw Mr.A was his mother/father idk and when his adopted parents found out they feared that he was traumatized by this new found information and they probably distanced him from the public because they didn’t want him talking about what he found out in the box or they are part of the organization and are keeping tabs on his son to see if he mutates or to keep Mr.A in check. Guessing by the last chapter it wasn’t Mr.A that asked him to come to the farm it was someone else who did. It’s obvious that Little A isn’t normal I thought he was a goat because of the lamb in his arm in one scene However there was pieces of lamb fur all around him so I think he may be a predator type of animal. Maybe a cat..or a dog but he has to be something unique to bare no characteristics to any animal and look human, but not act human. I think this a crazy science project gone crazy and little A is test subject 0. But this is my theory I really love the plot now it’s crazy I thought it was crazy smut hah but no. ヾ(☆▽☆)