I'll help you out by offering this common scenario:

You have an application which is a normal app bundle. It doesn't update itself because, well, few developers have bothered taking this route, so you download a new version of it and you throw the old one in the trash. Now all of your preferences are gone and you have to set everything up again.

That would not be a pleasant user experience, would it. Dropping the bundle in the trash doesn't remove your preferences because it would be an idiotic thing to do.