Limit glossification to selected content types and displays

I made an extra Text Format called 'HTML + Glossary' and only that format uses the Glossify filter. Would that solve your problem?

Indeed this may be a solution and even better that what I suggested (option to select bundles) but we will still need an option to apply or not to summary which inherits the text format of the main field (body). I think most people don't want to have summaries with plenty links. Also I didn't check how such glossified summaries appear in metatags or in other token based fields.

Our solution for this was to use Field Formatter Filter → and create a text format with only the Glossify filter. Then, we were able to add that as an additional filter for the fields where we want Glossify to work. Editors do not need access to the text format with this solution, and you don't need to change the text format of your content.