Options -> Playback -> Video & Subtitles
Check "Auto-Subtitle Stream", Language Country ID "English", Text Match "Japanese"
Options -> Playback -> Audio
Check "Auto-Audio Stream", Language Country ID "Japanese", Text Match "Japanese"
Putting Japanese for a text-match in subtitles may seem odd to you, but it has to do with the way Exiled-Destiny encodes their dual-audio MKVs. Normally with the right Language ID tagged to the stream, only the first option would be needed to select the English subtitle stream. But for some reason that I can't remember, E-D labels the subtitle streams as such: the English subtitle stream (which is empty) goes with the English audio stream, the Japanese subtitle stream (which is in English) goes with the Japanese audio stream.
So the above config will correctly account for E-D's subtitle labelling without screwing up stream identification for other encodes (hopefully).