Good questions. You're right there is no simple equivalency between R-series lay ups and S-series. Since shape drives so much of a tube's structural properties (see the "Materials and Shapes" Technical Presentations at http://cervelo.com/en_us/engineering/tech-presentations/ ), the layups end up different enough that they're hard to compare directly.
That said, there are still some overall principles (for example, SmartwallTM works in any frame shape), and Cervelo owners always get the "free" technology in every Cervelo (through Cervelo's intense engineering approach and long experience). By "free" I mean once we we've learned, it doesn't cost any extra for us to cut the prepreg in a particular (slightly different) direction, or lay the preforms in a particular (slightly different) position. The reason this is different with Cervelo is that very few other companies put as much emphasis on engineering analysis and testing as we do, as the existence of our Project California attests. Every Cervelo model has all the lessons we've learned applied to it to maximise performance; we never "dumb down" a model just to reach a price point. Once the knowledge exists, why would we do it any differently?
That said, when you upgrade from, say, S5 to S5 Team, you do pay for a better bike. The frame and fork are both upgraded in the S5 Team, through the traditional Cervelo engineering refinement process of selecting frame and fork materials and tuning the lay up to save weight. Since the S5 Team's project mission included the requirement to match the stiffness of the heavier S5, naturally that means we have to use slightly more expensive materials and techniques.
We know that for some riders, saving 80 grams isn't worth the increase in price, and that's okay since "worth it" is defined by you, not us. We just provide the options for those who decide it's worth it - for them. (Secretly I love the less expensive S5, since it has all the aerodynamic properties that make any S5 so fast, but saves enough money that some owners could consider a wheel upgrade, etc.)