Directory listing is nothing to do with Q2A, that's a problem with your server. You can add the line Options -Indexes in your .htaccess to prevent that (or preferably in the server's http.conf if you are able to). IMO you shouldn't clog up all the directories with blank index.html files (especially since anyone can download Q2A and know what the files are anyway).
You are right about those errors though - that file should be checking that QA_VERSION is defined, just like the other files in qa-include do.