From the back end I'm forcing a file type like this:
self.request['SESSION']['typeupload'] = 'RichFile'
So that when I upload a file, it is sent as RichFile, which is a custom type made for our project.
This works except when the option "Automatic upload on select" is enabled. Then, QuickUpload guesses the file type by itself instead of relying on typeupload.
Probably the file to look into is fileuploader.js. I worked around this problem by overriding the method qq.FileUploader.prototype._addFile defined in this file, replacing the line
this._queueUpload(id, this._options.params);
to
jQuery('#uploadify-upload').click();
which works for me but may not be a very clean solution.