I highly doubt that Samsung can speak for Best Buy and tell anyone that Best Buy will replace the standard wireless charger with the fast charger... If you read the fine print on the free wireless charger from Best Buy, they make it very clear the model number that they are offering for free (and it is the standard charger).
My wireless charger is also acting very flakey... I am on my second one... My first one charged my Note 5 for about 40 seconds, and then stopped charging... My second one keeps waking up the phone every few minutes. It starts up by lighting up the screen and displaying the nice graphic that indicates wireless charging has begun, and then goes dark...then every so often, the phone makes a tone, wakes up and the screen comes on again... Clearly something is wrong here...
I am hopeful that there will be some official program to turn these defective chargers back in, and trade them in for something that works (either the fast charger, or a standard charger with a fix).
My guess is that these standard chargers work with the S6, but for some reason has some compatibility issues with the Note 5...