Cervelo S2s were there in January 2009 for the TestTeam (the mold is the same as the SLC SL), but The S3 was new and not yet available. Remember S3s weren't delivered to dealers until after the racing season had already begun. So while the cost difference between S2 and S3 might not be large, switching to S3s after already starting on S2s incurs the full cost twice.
Now in 2010, the Team rides (mostly) the S3. This supports your point that the manufactured cost probably isn't that much higher than the S2. But again this year, as last, they apparently chose not to supply the team with both models.
Remember CTT was initially concieved as a low-profile "test" team for product development, and only after Carlos and Thor expressed interest did it seem possible to stretch the mission to include a higher level of racing. But I don't think the budget stretched as far as the good race results would have justified in a "non-test" team.