This is probably out of scope for your tool but it’d be nice to have built in n-gram deduplication where the tool strips any identical content from the header and footer, like navigation, when pointed at a few of these markdown files.
Your idea of comparing multiple pages would be a great approach. It would be amazing if you build something like this! This would enable so many more use cases... For example a better “send to kindle” (see other comment from rty32 [1]).