Given the constraints of the time when the format was conceived, the pdf format has a great design. I think, embedded designers should have a quick look on the PDF format to learn some tricks on how reduce unneeded memory accesses -- it basically implement a directory inside a file.
With the entry removal example, I was trying to show the format was not meant not to be shared. I know it is possible to remove data in other ways, and that probably every modern editor removes the data correctly. But it was not how the format itself deals with it. Of course, hiding entries with the flag had others uses such only print only the pages you currently working on without having to rescan the whole file.
I agree most devs don't have interest in learning how to do typesetting. But also, typesetting is quite complex by itself, specially when dealing with non western language. Luckily, projects such Harfbuzz (nowadays, hb is used even my emacs) makes it a lot easier.
Like I said in my original post, the format is anachronous. I don't think the format is intrinsically bad, I just think the format is not right for your time. I think we can do better nowadays.
PS: I've been thinking, it would be pretty cool to talk with the engineering team that worked on the first spec, and actually know what they were thinking back them and what they would change in it nowadays.