I would be surprised if the seller doesn't have a $500-1000 margin between the 2 basses as listed. They might take a $50-100 hit on the cheaper bass with the worn out case. The thing is, the people who would be up for buying the cheaper bass, are probably not the type who want everything "just so" and the somewhat beat up case would not really be likely to be as much of a factor as someone paying top dollar for a more pristine instrument.
In other words, including the nice case with the nice bass will attract the type of buyers who want that type of bass and can afford it, and the beat up case with the beat up bass shouldn't affect the price of that bass all that much (again, I doubt much more than the difference in value between the cases, which is maybe in the $50-100 range).
Also to note, this is not some hobbyist selling stuff from their personal collection, this is a buddy pair doing this as a "business" for close to 20 years (OP should have mentioned that, I never understand why people try to be so coy in threads like this, unless he's just trying to keep someone else from sniping the bass he wants). So their whole "raisin of extra" is to sell stuff to then buy other stuff to then sell. Not to get attached and hold onto expensive inventory when they have a nearly willing buyer if they make some small concession.
So I'd say there are better than even odds that this will end up being a mistake on the sellers' part, if for no other reason than it they missed their opportunity to say "ok, I'll do that if you round up to $2850 total for the bass, better case, and shipping" (shipping is $70 for anyone who missed that in the screenshot). Then the OP could either accept or make a counter offer, but whatever happened, at least each side gave it a good faith effort to make a deal happen.
And lastly, I have to disagree with some of the posters saying the seller's response was fine. What he SAID was ok, it's more about what he didn't say. The 2 guys behind the seller account are businessmen. Their (self appointed) job is to interact with customers in such a way that generates more sales, not less. So context is important. I would be surprised if most of the people making that argument haven't grumbled about a less than bubbly fast food cashier, etc... Customer service is important and it's kind of a lost art these days. So if I had the same experience as the OP, I certainly would avoid that seller in the future, maybe unless they had something that was completely unique that I really wanted that I didn't think I would get as good a chance at getting again.
I should also state that this is a bass model that's been in production for 50+ years, and surely getting a brand new OEM case is as simple as going online and finding a distributor (or going straight to the manufacturer). So really the biggest issues are just whether the price is worth it (take the beat up case more or less out of the equation, and factoring in an OEM case or decent gig bag at least), and ensuring that packing and shipping happens without incident.
So OP, ultimately your decision now is can you live with the case and/or justify ultimately spending about $3k total once you factor in shipping and a new OEM case, and also trust these guys who have numerous $4-6k guitars listed to pack a 40 year old bass properly to survive shipment? PS, if you were going to resell the bass at some point, if you buy a new case for it, I would include the crappy case with the bass, and sell the new case separately, I think you would net more that way.