There is a different ACF, RCF, VCF and User Messages File for each configuration. In addition, each configuration will have its own database, and hence the diagnostics, output and reports may differ between configurations. However, all configurations share the same source files, and so any options that affect which files are in the project (for example, adding files via Project : Synchronize or via the right-click menu in the Files Panel) apply to the project as a whole.
Projects with single or multiple configurations are allowed to upload their analysis results to either Dashboard or Validate. However, any project that is or will be unified (in Dashboard) or connected (in Validate) can only have a single configuration. This restriction is enforced.