As someone who has written a PDF parser - it's definitely one of the weirdest formats I've seen, and IMHO much of it is caused by attempting to be a mix of both binary and text; and I suspect at least some of these weird cases of bad "incorrect but close" xref offsets may be caused by buggy code that's dealing with LF/CR conversions.
What the article doesn't mention is a lot of newer PDFs (v1.5+) don't even have a regular textual xref table, but the xref table is itself inside an "xref stream", and I believe v1.6+ can have the option of putting objects inside "object streams" too.
Yeah I was a little surprised that this didn't go beyond the simplest xref table and get into streams and compression. Things don't seem that bad until you realize the object you want is inside a stream that's using a weird riff on PNG compression and its offset is in an xref stream that's flate compressed that's a later addition to the document so you need to start with a plain one at the end of the file and then consider which versions of which objects are where. Then there's that you can find documentation on 1.7 pretty easily, but up until 2 years ago, 2.0 doc was pay-walled.
Yeah, I was really surprised to learn that Paeth prediction really improves the compression ratio of xref tables a lot!