I spent a few days trying to reproduce anything near the anomalies present on that doc. You are quite correct that it cannot be done by any automatic mechanism.
There is one thing that absolutely proves intentional manipulation though, and that is the presence of cloned characters found in the doc.
BTW 30+ years prepress graphics pro.
You don't know what you're talking about. This is a result of the enhanced scan. I've provided examples in the past of the exact same "cloned characters" in other PDFs that were certainly not stitched together, and I can show you more if you'd like.