I would be worried about the same perception, it sucks but people do wonder when shadiness is unearthed, they naturally wonder what the other side of the story is. Personally I would probably not bring the issue to a head unless I was specifically questioned on it. I would save the Skype chat as a log of what transpired. Chances are the fact that you are on two applications will not be correlated, if it is I personally would give you a chance to explain the situation. There are a lot of us with multiple irons in the fire, that is most likely the perception they would have, there is nothing wrong with chasing two ideas, so long as you are willing to drop one to pursue the one that hits. So given that I don't think that even if it was correlated that it would immediately disqualify you from getting a call.

If you report it as soon as possible, I am sure it will be fine. You will be correcting a situation before they even have time to start evaluating John's application...

Also, announcing that you already have plans to submit your own application will make them realize you are not hiding any of your intentions.

I think you're overestimating how much they care. Being busy and looking at a ton of applications, they will probably just accept your email at face value, remove your name from the app, and move on to the next.