I worked there end of 2011 through beginning of 2012.....
We generally sold them at a discount as well. As a salesperson I was measured by my revenue per hour and Apple products always were the highest.....
This makes sense if you think about it. Generally speaking, Apple marks their prices up to increase margins even though the cost to build the device isn't much higher than the competition. There is more "profit" to go around (I'm not saying Apple doesn't retain the lion's share of this - they definitely do, just that because of the "Apple Tax", retail outlets see higher revenue on their products as well - just not to the same degree as Apple does.)
The fact that Best Buy and Apple have a relationship could also be a factor as you suggest - I don't know. I was just a salesperson