Regarding your query, The behaviour is happening because the EDD Rules are getting applied at that moment.
According to the DITA Template, the default font is Calibri. Since it doesn't support Korean Glyphs, the Glyphs are getting replaced as ?.
If you are certain that the Authoring has to be done in Korean throughout the document, You may have to replace the Calibri font with a font that contains Korean Glyphs (like Batang Font) in DITA Templates.
Please note that it can be done conveniently with the help of Fonts Panel (View > Panels > Fonts...) where there is an option to replace the font family.