I didn't mean in the Scripture Reference settings, but when you enter a cross-reference in the text of the glossary entry. So instead of say \xt Mat 5:12\xt*, which might expand to Matthew 5:12 if the short name is Matthew, you would have \xt Mat 5:12|Mat 5:12\xt*. The idea is that what is to the right of the vertical bar is what appears in the formatted version.