So I managed to find a Live Wallpaper that I could set it to be very dim that works with Daydream and I tried this solution.
First it does work - no more charging issues and with the Live Wallpaper I am using the screen does not heat up.
I also found that if you plug in your phone (for overnight charging) and turn the screen off before daydream starts up, Daydream does not turn the screen back on.
Some of you may have known this, but I did not and I was very happy to find this out.
This works for me. I actually like having daydream on when on the wireless charger. My biggest issue I have had so far with the Note, is that when a notification came in, it would flash the LED and not show as charging, this bothered me that I couldn't tell that the phone was charging especially with the Wireless Charging issues I had been having.
Now as long as Daydream is on, I know it is still charging and I can shut the screen off when I plug it in at night.