Content assigned to a course template does not get copied into a newly created course offering that lists the template as its CourseTemplate. If you want to store content in a course template and then copy it into a new course associated with that template, you can use the course content APIs to inquire about the template's content structure, and replicate it in the newly created course: the Content.ContentObjectData JSON blocks you use to create new content structure are a superset of the Content.ContentObject JSON blocks you see when you ask about the content structure.
Unfortunately, because of the rules around an org unit's file content store, we really don't recommend that you put actual file data into a course template's content store, because there's no easy way to refer to them from child course offerings, or copy them remotely into the child course offering's content space.
If you do store file data in the template's content space and want to put it into child course offerings, you need to fetch it from the LMS to the client and re-upload it into the new course offering.
You may get more leverage out of storing common course data objects in Desire2Learn's Learning Object Repository where what you put into the course template/offering's content structure are links, not files.