Oh yes, definitely. I think this is why Mozilla has not made this the default behavior in Firefox; there will always be the risk of false-positives breaking copied links, so it's important that people know that there's some kind of mutation happening.

ClearURLs uses a JSON file with site-specific regex patterns and rules. In theory I could customize this for myself, or better yet submit a pull request on their GitHub. If I have time I'll look into it.