iPhones don't have wireless charging so I can't see a problem. I doubt if the charger senses a compatible unit, it just bangs out the inductive stuff anyway. It's not a new system, electric toothbrushes have been using it for years.
What is not clear is whether the USB sockets provide a charging current, if they did, and you assume that you would always be plugged in to use Car Play, you wouldn't need a wireless charger anyway. If it doesn't provide a charging current, then wireless charging would be useful (if your phone supports it) as the battery will go down pretty fast if it is plugged into Car Play. The USB socket on my Leon seems to have a tiny current that will keep my Satnav running, but it won't charge the phone.
The one thing you must not do is put your credit cards anywhere near it which could be a problem if you have a phone case with your cards slotted in.