OK yeah, I will probably just need to replace the charger in the armrest. I am still under warranty for maybe a couple of months, but I flashed my ECU and my service rep says he thinks that will void my warranty. Oh well.
As for the heat, any Qi charger is going to make a phone hotter than a lightning cable. I would not change out the charger because of heat. Heat just means it is doing it's job.
Qi charging Blog