With a traditional listing, the buyer will assume that the seller is willing to negotiate a 10% reduction in price.
So if you want $45,000, you would list the vehicle for $50,000. You see this a lot on autotrader, etc. for private sales.
In this case, the $41k reserve that BaT recommended is only 9% different from the seller's desired sales price.
BaT doesn't set the reserve, the seller does, but Bat reserves the right to not list the vehicle. If the seller doesn't like the suggestion, they negotiate or just go elsewhere. This is true of all auction houses. One way to negotiate a higher reserve is to pay for professional photographs and detailing.
BaT writes up the vehicle listing, so they have skin in the game in the form of labor hours. The write-ups are quite thorough. The objective write-ups combined with the pre-sales data from previous sales leads to BaT buyers being better informed than eBay buyers. I have found eBay listings to be highly suspect. Craigslist listings are just silly bad. When I have seen comments in BaT auctions that the seller takes exception to, it's typically the case that the comment is accurate but inconvenient for the seller (read undisclosed). I have seen BaT dispell bad comment information using additional photos or documentation, but the reality is that most of the comments are actually correct or easily corrected by the seller in the comments. The seller that is offended easily or emotionally invested is probably better selling on eBay where such communication is private.
I have sold cars on BaT, eBay, Craigslist, and private listings.