My theory is Peter is/turns into September.
Unless Joshua Jackson began gene theropy to become Michael Cerveris by the end of the season.. I'm gonna go with, no.
Peter "becoming" an Observer was completely a nod to the fans who have been around since the very beginning and followed Fringe a good bit. During season 1 Peter showed up at comic-con dressed as an observer.. him putting the tech in his body was just a nod to this.
I also believe if we had had another season, we might have actually had a full fledged 14-21 episode arc with Peter having the tech in his head.. and looking a bit more like an Observer over that time, but lo they are short on time, I also think we might have seen this in the past, and not in the future.