To be fair, a base Model S doesn't have all the autopilot stuff and upgrade sound and everything else. So to compare equivalent equipment packages, that Model S is a lot more than $9k more.
doesn't the model S though also give you free access to superchargers (unlike the model 3 where you have to pay)? This should factor in the comparison if you live close to one and/or plan a lot of cross country trips where they are available
The value of free Supercharging is fairly small for most people. If you drive 12,000 miles/year and 25% of your driving is Supercharged, you'll end up paying something like $100/year in Supercharger fees for a Model 3.