yes they can charge your card in advance of you getting the rifle, what would normally happen IF you failed the background check, they would refund you either ALL or JUST some of the money, and charge you for the check!
rifle then would be put into there inventory, as the gun is NOT yours till its logged out of there records to you at time of the paperwork being approved!
all you did was basically pay in advance for the gun, and that assures them its SOLD, and there not stocking a gun they didn';t plan to.
like I said, if you fail, they can charge you a stocking fee or likes, and for the check!

I WAS a gun dealer(had business and FFL and a Class III dealer as well, and an explosive's lic) for many yrs too, so, unless something I don't know about changed, this is what will happen!
they DON"T have to charge you either for anything, but most shops will due to they now have a gun they didn't maybe want to sit on till it sells?