As you've by now discovered, the Quick Preferences plugin won't allow you to change Save to Disk templates.
Do you need to export certain books with one template and other books with a different template? If so, you might be able to use the Switch function in your Save to Disk template to choose between two different sub-templates based upon fields in the database. For example, you could set up your template to export Epub books with one sub-template and PDF books with a different sub-template.
Take a look at
this thread for more info. I use it to set up different templates for my different libraries, but the concept should be the same for working with books in a single library.