I would think they could do PayPal for everything. You send them the specs, they send you an invoice via email for the total and you make the PayPal payment to firstname.lastname@example.org. If you don't send them the money they don't start working on the stuff. If they wanted to get really fancy they could have a "click here to pay for this order via PayPal" link on the invoice email.
The Warmoth website is still somewhat behind the power curve in general for online sales, but if they wanted to, they could totally automate the pdf order form system they have going now and eliminate a lot of tedious manual steps. I'm glad for the upates that they have made recently, though. +1 for the Paypal.
I'll say this-- if they had PayPal for everything on the site I would be BUYING a LOT more Warmoth stuff... The process of having to fill out the PDFs, print them and fax is so slow and laborious that I usually change my mind half way through and never send the order. If they had PayPal on everything I would buy the things before I was able to talk myself out of it!! It would be interesting to know how much they lose in sales annually just because the custom order process is slow.
In grocery stores they know that the way to get you to buy something is to get you to stop and look. If you don't stop-- you go straight in and get what you need, you are way less likely to impulse buy. So if Warmoth were to make their custom order system more impulse-buy-friendly I bet they would see significantly more custom orders. Making a customer order nearly as fast as buying from the showcase should be a priority, I would think. It would be a good thing for them and for the customer.