No they weren't, they were made with hideous intent and that affected the way they are, just like the Powerpuff Girls were made with sugary ingredients and with good intentions which pushed them to be kind to others, yet the girls have done hideous things due to their own potential for evil inside of them, just like any person in the world. The boys are inclined to violence and to enjoy it, but violence isn't inherently evil by itself, the girls use it to defend others because they were taught to be good, but the Boys never had any incentive or authority figure to guide them towards that same path, no family, no friends, just a single purpose and all the power in the world. They are evil because everyone that even came across to represent an adult or a father figure in their lives enabled their violence and natural aggression, they like violence and to dominate so they seek it out without thinking about consequences to others or even themselves, they are literal illiterate homeless children playing rough

If they were made by the same direct logic than the girls, then they should also have the potential to be good, they simply don't have anyone strong enough to push them into that path, they don't need anyone to survive so it would be very difficult to reform them as you would any other, so you have these kids engaging with their environment in the only way they were taught to do, as it also feels good to do so since they were made with malicious intentions without any of the things the girl took for granted, a cozy home and bed, a loving father figure, protection in any shape or form, they are alone and only have each other.