Matt,
The glossary is set up so that the small window "title" (concept) is the word or term and the larger window is the definition. The auto linking works on what is in the "title" (concept). Picture from using glossary page.
Glossary
Glossary Term Linking
གྲོས་བསྟུན་འདི་བསྡམས་ཡོདཔ་ལས་ ལན་གསལ་བརྐྱབ་མི་ཚུགས་