Is there a way to imbed Link files (photos, in this context), so that you can take a given work (1 .indd) and not have the Preflight detect it, without having to turn it into a PDF?
A document would come up, on a different machine than created, and look just like you desired it to, but have the Preflight tell you that 52 Links were missing, for example.
Any help is appreciated.
You should never embed linked images as it is the most often seen cause of file corruption. The best way is always to give away a PDF/X-4.
If you need to pass on open file, go to File > Package… and send the package to the recipient.
When your transfer an INDD file containing an embedded link, the content of the link which is a photo in your case, becomes the part of the document itself. Since the photo is embedded in the document, it cannot go missing, hence preflight will not need to scan for missing links when links are embedded ones.
I hope, I have understood your query correctly. If it is not what you intended, please revert back.