Sounds to me like that's more of an issue with the PDF specification than with the work presented in the paper, in which case that's hardly the metric by which we should measure its merit.
I’m not saying PDF is a good format. I’m pointing out that they’ve made a poor choice going for PDF. There are other formats they could’ve used to demonstrate this specific technique. Like OTF/TTF which is a more traditional binary format with a whole range of approaches, including offset tables.
The abstract says "We have used IPGs to specify a number of file formats including ZIP, ELF, GIF, PE, and part of PDF". Sounds to me like they threw PDF in there to test the limits of the technique _after_ using it on a bunch of other unrelated formats.
In fact, the authors state "PDF is picked because it is the most complicated format to our knowledge, which requires some unusual parser behaviors. We did not implement a full PDF parser due to its complexity, but a functional subset to show how IPGs can support some interesting features (...) PDF is a more complicated format. Our IPG grammar for PDF does not support full PDF parsing but focuses on how some interesting features in PDF are supported. As a result, the parser generated from our IPG PDF grammar can parse simple PDF files"
Kinda sounds like you didn’t read what they actually wrote in its entirety but have still taken the first possible chance to jump in and quite aggressively tell them how what they’re doing is wrong.