If copying and converting a Blu-ray to DVD take same time, it seems DVD converter engine is slowed by HDD access times and low CPU usage is totally normal.
If you want to merge a subtitle track (forced or not) in an MKV file, you need to create your custom profile...
In custom profile selector, just set the subtitle track type as 'Merge subtitle in video'.
With this new profile you will not be able to select more than one subtitle track in same time, but it will be merged in video stream, not as separate DVD-VOB subtitle track.
EDIT : I think all your questions are helpfull and should be asked in a new post to be more visible... (we are reaching the 6th page