Is there any way to change the output filename for qlmanage?
You can use textutil to convert Word documents to HTML and specify the output filename; it uses a different converter, though, which may not be acceptable for your uses.

With regard to qlmanage, you're abusing Quick Look here already.  The output is a directory, not a file, which is only designed for Quick Look to consume.  That Preview.html is a fixed filename is by design; otherwise the Quick Look displayer wouldn't know where to start.  That you're able to extract the HTML output yourself is a nice side effect, nothing more.