Yeah, I don't think he said it in a sense that he thinks he sucks, doesn't think they're friends, or any of that. He was stating his opinion (in private) what everyone in the world already sees. He may be overstating how much time he truly has left, as well.
And his own expectations for himself are probably exaggerated by his competitive nature but I wouldn't put another 5 years past this man.
Edit: I also hope little things like this, that aren't meant to be an insult, don't destroy his friendships. It's fairly well known that Tom and Peyton are kinda-buddies outside of the sport and have great amounts of respect for each other.
Be a shame if this put tension on this friendship or any others as a result of these emails.