... IMHO this was much better as the subtitles are a pretty big distraction
It only embeds them if you choose the single file format option, and only if you choose to keep subtitles. If you un-tick all the subtitle tracks then you will get a copy without burnt in subtitles.So in summary, for now CloneBD ALWAYS embeds the title regardless of the format.
This is very unfortunate.
At the beginning, there was no title at all. In many cases, IMHO this was much better as the subtitles are a pretty big distraction.