"Prime numbers are what is left when you have taken all the numbers away. i think prime numbers are like life. They are very logical, but you could never work out the rules, even if you spent all your time thinking about them"

I think Christopher does this because in his eyes all the prime numbers are like 1,2,3 to him, so it would make sense to number all these chapters in prime numbers. This is his little touch to his book. He says you can never work out the rules, even if you spent all your time thinking about them.
I think Christiopher is so mathematically inclined and that is most of what he knows so he compares it to life, because you can get to know someone but you will not know everything about them. Even if you spend all your time thinking about that person. Thats why i think he compares prime numbers to life. Life is very hard to figure out, just like prime numbers.