My understanding and explanation of this issue was incorrect, sorry. Linked images/resources are meant to make smaller .afpubs than when embedded. Embedded documents are embedded (with a preview for render speed). Linked documents will store a preview of the linked file, but currently due to a bug they store too many previews and increase the filesize. Currently linked files also store the file (as well as too many previews), but this is a work in progress. I will try to be better informed before I post next time.