The biggest negative of this way is that if you have one specific feature you really want, sometimes it will costs thousands to get it because it got bundled in with a bunch of other features you didn't want.
Looking at the S order page however, it is already pretty lean in terms of options (esp. ones that are purely hardware):
Autopilot $2500 (software enabled)
Premium Package $3000
Air Suspension $2500
Subzero $1000
Sound $2500
Rear Facing Seats $3000 (not applicable for 3)
High Amperage Charger $1500 (software enabled)
Order your Tesla Model S | Tesla Motors