Are they keeping the Bitcoins, or just exchanging them for fiat?
They use BitPay as payment processor so likely converting to USD instantly, although they could be keeping some % in BTC if they choose to.
From their site, if paying with bitcoin:
All Bitcoin Orders Receive a 4% Discount Relative to Credit Card/PayPal Pricing
If paying with paper check:
All Paper Check Orders Receive a 4% Discount Relative to Credit Card/PayPal Pricing
If paying with bank wire:
All Bank Wire Orders Receive a 4% Discount Relative to Credit Card/PayPal Pricing
So, the "discount" is only a discount against credit card/paypal not against other methods of payment. I've never bought precious metals with anything but a bank wire. As a side note, bank wire is currently not available for them for some reason. I need legal confirmation that the money arrived. When using bitcoin, how do I prove the bitcoins were received by them? Unlike a bank wire, I'm not sure how well the court system would deal with hash addresses if there was any issue. And, as a final comment, I get bank wire transfers for free so I would pay zero to buy using a wire where I would pay a small transaction fee to use bitcoin. The cheapest methods to purchase are paper check (zero fee) and wire transfer (if you can get zero cost wire transfers).
Yes, as stated in OP you get 4% off compared to cc payments (and PayPal). That makes BTC payments the fastest (and cheapest for many) option.
You'll be paying via BitPay so you'll get order number + email receipt, similar to paypal, except you'll also have blockchain tx id as an extra proof.