Hi, I think you have this a bit wrong and I hope you don't mind me making some clarifications. Layered documents can only be modified on the layers to any expert degree with programs such as Photoshop, Illustrator, InDesign. I'm expert level in all of these applications. When I create a document starting with these programs, I can output the file as a PDF for review or as a final printer's document, and so on. If I didn't merge or flatten the layers before outputting to PDF, then the document might be able to be opened in one of these original software programs so that further editing on the layers could take place if needed. Not all PDFs are importable into those programs, and some conversion will take place, especially if versions or platforms differ. Usually I can open anyone's PDF in Photoshop or InDesign, but those files don't always all behave the same.
Anyway, in my experience, it is not standard practice to send a PDF to an end user for making more modifications on that file. I don't want anyone to be making a version outside of my control anyway, especially in a separate software application (unless I didn't care to be the master holder of the most recent version of the document). In fact, it's very clunky to make changes to any PDF using Acrobat and that is what most end users have (and then it's typically only the free Reader, not the full program). If I wanted the recipient to be able to modify my original file, I would send the native file. Why would we go back and forth with PDFs, only to have them have to be reconverted in another program? (I admit I am only familiar with Adobe products, perhaps you use another PDF software editor?)
IIRC, what investigators discovered with the BC PDF was that after they opened the file in Illustrator, the layers were visible. I agree that the receiving party, not knowing anything about layers, approved it and ran with it! Which begs the question, did the forger intentionally leave the layers in the PDF unmerged because they wanted them to be discovered? Because it's a stretch for me to think that the forger would be using these programs to create layers and then not merge them before outputting to a final PDF. But they might have been rather rushed or just forgetful. The mystery continues...
The most interesting thing will be seeing how this forgery will be viewed in the near future. Ten years ago I took Photoshop in college graphics design courses. But now students in middle school are skilled in these photo editing programs! When this technology becomes practically common knowledge, how silly will this phony birth certificate fiasco look?