What works best for me is to tell the Finder to copy the file to the clipboard. The finder takes care of all the details, different file classes etc.

osascript -e 'tell app "Finder" to set the clipboard to ( POSIX file "/Users/someuser/somefile.zip" )'

You need to provide an absolute path and e.g. avoid "~" (home directory).

I tested this with pasting to Finder windows, Apple Mail, MS Word...