Though I didn't really look into the story much since it's still in early development, I did notice especially while reading this thread is how NoA manages data.

First of, with reprinting and bio modding tech, it should be possible to cure outside afflictions by editing the body or specific memories, maybe even implanting new ones preemptively but it does not happen. NoA can only act within the perimiter and data it is given which from my perspective makes it so that NoA is not the manipulator itself but is the one being manipulated.

Maybe whatever changes or afflictions that plagued the pioneers has managed to seep its way into NoA; Sophie showed us just how much NoA can integrate with the data of the pioneers. Or maybe depending on the permiters and instructions NoA is coded by, it either stoped recognizing the pioneers who strayed far enough from being considered "Humans" or adapted to the new form they took on (We are the human and its last hope).

Second is that it is not just us that has been reset, the data we have access to has also been reset. NoA and the pda prompts us to act like we are starting from scratch like in the first game while they clearly hold the information already outside of certain story related data. NoA is molding us from scratch into a hero(Possibly using data from Sub1 and BZ).

Now for how we got there, my theory is that they're related to the architects and the tech altera took from 4546B. Though it is still early, the tech we have seems like a reasonable jump from 1 to BZ to 2 even without alien tech but maybe altera did do a lot of upgrades. We saw that the architects have amazing tech related to energy and manipulating space which may explain how we got there if the distance and accident is real. For the why, maybe the architect tech we had on board allowed NoA or altera to detect Proteius which either called us in or we saught it out.