Sometimes it is useful to change the preference values during deployment time, because preferences hold environment specific values. Actually, this is pretty easy by using composite deployment configuration plan(s). One for each target environment.
Right-click on the composite file and generate a deployment configuration plan for your composite. When you open the file, you will find a search/replace construction for the preference.
Now change the value to the environment specific value, save the config plan and use the config plan during deployment to a specifc environment.