The short answer is "You can't". It is not that you can't change the settings in Chrome. You can. It is that so many applications exist that will simply go in and change your Chrome settings to suit their needs. Thus all the work you do to limit the creation of temp files can be undone in the blink of an eye without your knowledge. Sweet, eh?
Your best bet is to get CCleaner and run it often. (Once per day) CCleaner will clean those temp files out.