five simple steps to profile enlightenment
This assumes an all RGB workflow and doesn't consider CMYK issues when preparing files for an offset press.
If a job is going to one known destination press there are cases where the CMYK values should be protected—you want deviceCMYK. InDesign's Color Settings and export options accomodate those needs in a number of ways. In Color Settings there's the Preserve Numbers (Ignore Linked Profiles). The PDF/X-1a standard exports all color as flattened deviceCMYK or Spot. It's up to the user to correctly set the export options, there's no setting that works perfectly for all needs.