When I ordered my Cross Check, it was similar. No shops stock them so I couldn't test ride one. Luckily I have a good relationship with the gang at my LBS, and used my fit session to narrow down my choices based on stock setups vs. my fit numbers. There was very little which needed changing on the Surly.
The non-refundable deposit seems a bit severe, IMO. Especially if you're narrowing it down to 1 or 2 bikes which you're looking at, and you're going to buy from that shop.