Consider a document as 'unsaved' (dirty) when a linked image gets updated
Illustrator think that updating a link is not an operation.
This leads to problems with documents that use PDF-compatibility option.
Imagine you have an already saved document that have some linked images in it. You open it in Ai and then Edit a linked image in Photoshop. Make some changes in the image, save them in Ps, go to Ai and agree to update the link...
But Ai still considers the document as non-'dirty', as if no changes were made.
You can’t save the document and re-write the PDF content, to see these changes appear, say, in the InD document, where this Ai-documnet is placed in another document. You can only re-Save-As is, which is a not convenient operation. And if you close it — Ai does NOT offer you to save! And you have a document that you though HAVE an updated image in PDF-layer, while in fact it does NOT.
InDesign treats this right in same circumstances.
Again, if you had an .ai document that uses a link, that has been updated before you open this .ai document — Ai will tell you nothing about the change, and you have a file that has two version of image — one in Ai layer, and one in PDF one.
Very error prone.