OH my goodness, this is true. I feel my age too - yes, I remember working on the first release of Pagemaker. I still hope Affinity does the package project part. It means a lot especially if it has a lot of fonts and files involved. I just finished a 200-paged, image-heavy booklet. Had to do it manually, that is, create a folder for the PDF, FONTS and IMAGES.
One reason why it helps is that, clients I've encountered usually pick and drop pics. While I'd put all pics in one folder, sometimes they'd change the pics for something better. Not just once or twice, but several times. It would help if it could move pics that were used and leave the ones that weren't.