Yes, they can - normally these are zipped up by you and the publication wizard creates a "second version" that doesn't include any executable files which runs alongside the EXE version.
I think that you want to create a slightly different version since it would seem that yours won't work without the EXE files present. I don;t know how to do that, but I know a man who does...
If you post this request here:
http://www.codeproject.com/Forums/1641/Article-Writing.aspx[
^] Sean reads everything there, and he can either do it for you, or tell you how to do it yourself.