You shouldn't really need binwalk given how zipfiles work with the directory at the end of the file. You should just be able to unzip the file as-is. Though I suppose that could vary based on what you're unzipping it with. They should support it, though, as that's how a self-extracting zip is supported...ignoring any extra bytes at the top.

The zip on Linux has "zip -A file.zip" functionality that will strip the non-zip preamble too.