I'm not sure why but it seems the point of the system has completely gone over some peoples head's. The system is there to improve a person's life. Noah went from someone with absolutely no motivation to a medical genius who saved millions thanks to the system.
When he died he asked for not the current him to be reincarnated as he felt content with his already completed life. Instead, the younger him, the one who initially had those dreams of a new exhilarating life could get his wish. As for what the custom order means. Kosuke will have the memories of Noah Moore up to the first time he encountered the system. (So he only knows things about his previous life up to the age where Noah was 15/16.)
Also, Just because one gains memories in no way means that they are the same age as the person in their memories. When Kosuke was 5 his mindset was 5 it's just that thanks to his memories and various talents he was far more intellectual and mature.
I hope some of this clears up the confusion. Mc is not some 80 year old pedophile hitting on young girls. He is a 15 year old with the memories of Noah who was also 15 and the various anime that are now his reality.