First of all, John is my favorite character in the game. He is the only one who has remained unchanged no matter the circumstances. Now, to answer your question: in Part 10, when the MC and Silvia visit the clothing store run by Alicia, she raises a very important question — why would John appoint a male in his office? She is surprised to see the MC, as she had never seen any male worker at Magic Grand. All those who work there are alluring women, and we know what purposes John uses them for. So, unless there is a very special reason, John would not appoint the MC.
I personally believe the MC is John’s son. Though we don’t have much proof to support this, there are some hints. One of those I just mentioned. Another is John calling him “son.” And if you remember, Alicia also mentions more than a couple of times that they both sound similar. Also one more thing I believe Chloe is not John and Nichole's daughter.