[eschwartz]

You can use the in_list() function fro the manual to see if a specific format is available for that book, and modify the filename save template based on that.

The filename save template has a default value set in preferences, but if you have configured your device (see screenshot) you will need to set it there additionally/instead.
That manual page applies to any templates in calibre -- templates are used in Bulk Metadata Edit, sending to device (both filename save templates and plugboards), custom columns built from other columns... however, NOT for organizing the library on the filesystem. You have no control over how calibre stores its own internal copies of your books.

...

Plugboards have absolutely nothing to do with filenames. They cannot affect filenames in any way.
However, different ereader apps/devices use different methods to show your books. Some use the metadata (modified by plugboards) and some use the filename (modified by filename save templates).