In such cases, we use the approach of creating an Install Profile for the project, that enables us to select, install and configure the requisite modules, create content types, create roles, set a theme, and populate the site with some representative content.
In fact, the experience has been so positive that it has fast become the preferred method here at i-KOS. This process has the distinct advantages of:
making all configurations, that would be hidden in the database, visible in code
ease of rolling back to a previous point during the build phase (as minds are changed and/or developers had a bad day (yes it does happen!)
allowing us to hand over the 'code' at each release and at the end of the project
This profile is separated into platform-specific and site-specific features. Platform features such as picture uploading and cropping, social integration and back end moderation, can easily be updated across all sites without affecting any individual site features.