Hi The-Dude,
I talked with my colleague to answer as the best way to your question.
Duplicate content is based on the fact that the tooltip can include the same content that is available in other page or in the same term page.
Our plugin enable to manage this with a feature to set the excerpt words (or characters), to disable the link to the glossary term and so on.
Search engine identify duplicate content when is everything the same content but because you are using an excerpt this doesn’t involve this case. Also if your tooltips are only definition in a sentence as example, doesn’t involve again this case.
Or you are using the terms without the archive again is not involving the duplicate content, or using all the various features doesn’t involve again a duplicate content because every page is different.
So mainly is based in your SEO strategist and features that you want to offer to your users where you can balance this based on your needs.