I would add a comment, partly to signal to a reader that the file is not "vanilla", with links to any relevant documentation or an issue tracking system.
Edit: So this situation reminds me of when a Linux distribution packages e.g. a library. Debian has guidelines and standards around how packages should be built and named, which could well vary from how the library is usually distributed pre-built.
I don't think you should be shy about naming / building / modifying a library, since I'm guessing you won't be distributing the result to the wider world? In this case I would include a README along with the source that describes what changes you've made and why. E.g. README.${companyName}.changes