When I was active in BR and varmint hunting, I had a few custom rifles made. The gunsmith with whom I worked with most would charge me enough up front to cover his material costs incurred. I think that's fair, since it was usually several months until the rifle was built.
A retailer has no cost incurred in an order for a standard production rifle, and usually has 30 day terms on the inventory payable. So any up front charge is simply an interest-free loan for the dealer. If it's a specialty item, then a reasonable deposit is not unusual or unreasonable.