I got told to pay a fee of about 40$ and also that they had to reserve the same amount of money as an Iphone 5 costs if i want a replacement phone while mine is in the service-shop. Sounds kind of weird to me..
If you are using one of the included "incidents" on an Apple Care+ warranty, the $49 price would be correct. As for the credit card hold for the cost of a new device, that is standard for any "advanced exchange" program. Most HD manufacturers also do the same thing. They basically charge you for a new device, and send one out to you, then when your old one is returned, and found to meet the conditions of the exchange, they refund the original charges. I seem to recall that sometime around the launch of the iPhone 4, that Apple did start charging for shipping on any advanced exchange units, so that might be the "about $40" charges you mention as well. The Apple Care person on the phone should send you an e-mail with the details of what is going to happen if you elect to do this.