There are several reasons you might want to modify default search paths or the location of program files. For example, if you prefer to use a third-party plug-in instead of a similar plug-in installed with your product, you can reference that file and avoid having to add it at each workstation.
Another example might involve default file locations that have changed in the new version of your software. You can modify the location of the files to be the same as with an earlier version.