I do not think a lot of people funded a phone with the idea of putting it on eBay. The return on investment takes a long time and is a bit risky for someone with no other purpose for owning this kind of phone. Even if the only motive was profit, they at least helped fund the development and manufacturing costs. If they buy a phone now to take advantage of the lack of supply, they will probably not get their costs back, which will have to include the cost of shipping it again. By the time the phone is received, Purism will probably be very close to being able to ship a phone within a week or 2 for an order placed now. Privacy minded people prefer to buy from the source, so they may end up selling at a loss.
When you list something on eBay as an auction, there are 2 things that determine the price: The initial price, set the by the seller, and the second to last bid, set by a bidder who did not win. The seller is not in control of that last part.
I get that not everyone wants to deal with eBay, especially as a seller, but listing unwanted phones is a better option than asking for a refund, for both parties. Perhaps if more did that, the supply on eBay would be higher and the bids would be lower.