Without wanting to get too far away from the original issue - it's relevant when talking about embedded/linked images - I think there is something else that needs to be considered.
When a document is to be sent to a print shop (or anywhere else) it can be sent as either a PDF or as the document in its 'raw' AFPUB form (as long as the print shop has a copy of Publisher).
If the file is sent as a PDF then there should be no problem printing it as the PDF contains everything needed for printing.
However, sending a 'raw' AFPUB file has some extra issues:
1. If images are linked to the document - as opposed to embedded - then there needs to be a way of extracting/copying the required images from the user's machine for inclusion in the document at the print shop;
2. The folder structure - from the user's machine - that contains the extracted/copied images will need to be 'flattened' at some point in the process as the user's folder structure will probably not exist on the print shop machine;
3. This means that - for the print shop to get an AFPUB file that shows the linked/extracted/copied images correctly - a slightly different AFPUB file will be needed as the links to the folders/images will need to be changed to accommodate this 'flattened' structure;
4. This means that the AFPUB document that goes to the print shop will need to be different from the one that that user has been working on.
Alongside this, fonts also need to be considered:
5. Any fonts that are used by an AFPUB file will need to be extracted/copied from the user's machine and similarly put in some kind of 'flattened' folder structure;
6. The AFPUB file may or may not - I don't know how it works - have to be changed to pick up the fonts that have been extracted/copied so that - even if the print shop machine has those fonts - the correct fonts/versions from the user's machine are used.
All-in-all, if an AFPUB file is to be sent to a print shop - rather than a PDF, because of file size or whatever other reason - then there needs to be a way of extracting/copying the image and fonts used in the document in a way that makes it easy for the print shop to re-create the document without making any changes at all.
And there may be issues with colour profiles too but I don't really know much about them.
To put all of that another way: If you link to images, rather than embedding them, and if you send the AFPUB file to someone else, there needs to be a mechanism where the linked images can be taken from one machine and the document properly reconstructed on the other machine without the user on the other machine having to do any work. Otherwise, what you get printed may not be what you designed.