> It's automatic. As if there were no page boundaries, like in text diffs). But for a paged-based diff-tool it would already be quite useful, if the user could interactively specify pages to ignore, so that the comparison can start again where both docs are the same (e.g. at the start of the next chapter).

Gotcha. I might transform this project from a command-line only to a visual tool. I could implement that, thanks for the idea. I can actually have some sections of the PDF ignored.