Some properties are not so important to save like window size after resizing it. Some other properties should be saved and in that case, you should call [font=courier new]setModified[/font] method.
Prefer to use properties with a unique prefix to avoid any clash with future ones or properties managed by other plug-ins.

Note that these home properties are saved for a project, not for all projects like you seemed to want by speaking about "preferences". As you noticed, there are no [font=courier new]setProperty[/font] / [font=courier new]getProperty[/font] in [font=courier new]UserPreferences[/font] class at the moment, but can save additional data at the same place as where [font=courier new]preferences.xm[/font] file is saved if needed.