I know this is an old thread, but I found it very useful! I'd just like to add for any future forum users out there that any transcoding in progress must be restarted after changing the settings. There is no 'apply' button and this wasn't obvious to me (I was wondering why the transcoding was taking so long).
If this is read by any developers, I'd suggest having a prompt offering to restart any transcodes in progress with the new settings or something along those lines.