DITA maps and projects can be set up many different ways. The default output formats (and their mappings from elements) included in the DITA2Go distribution reflect only one possible configuration. You can find and inspect the default element paths in distribution file %omsyshome%\d2g\configs\system\d2g_config.ini.
For example, for glossary content for Help systems, DITA2Go covers the bookmap case. In d2g_config.ini:
[BlockFormatMaps]
title/$topic/glossarylist/booklists/backmatter/$map/1=GlossaryTitle
glossterm/*=Heading1
glossdef/*=Abstract
And in d2help_config, Heading1 is one level under GlossaryTitle:
[HelpContentsLevels]
GlossaryTitle=2
Heading1*=3
so the glossary terms nest under the glossary title.
However, if you have the glossary nested under a top-level topic, the glossary terms are at the same level. The fix is to override the default mapping and lower the glossary terns one level: