Preference files retain information about the default and custom settings for a particular application. Also, they store information accumulated over time not directly related to a preference setting.
In Safari's case, this retained and accumulated information comes from a variety of sources within and outside of Safari. For example, 3rd party add-ons, such as
Glims, store information in the preference file pertinent to their operation and settings.
Sometimes, corruption occurs if this information is incorrectly coded in the software. In that instance, as Safari accesses the preference file, it will crash due to a flaw in the data stream. Another example - updating Safari from one version to the next might trigger corruption if the 3rd party content within the preference file is not compatible with the new version's operation.