It was fully addressed in Brisson's 'X-Force' where Stryfe and his Krang-Trio broke Ahab's conditioning on Rachel to use her as their puppet to track/kill the Askani. But then Mother Askani appeared to Rachel and helped give her the strength to free her mind from everything.
I mean technically yes this is the same Nate that she had/s a psi-bond with. It's how Rachel (as Mother Askani) was able to communicate easily with Nate as he was growing up. Whether or not any writer will acknowledge it (Brisson didn't) moving forward is up to them. But it's the same Nate, just an earlier version than the adult Cable she discovered the bond with (Excalibur #71)