How can I activate SEO Glossary in Yootheme ZOO?

In order to activate SEO Glossary definitions in SEO Glossary you need to activate content plugin in content type:
Components -> Zoo -> Settings tab -> For exemple Cookbook -> Hover to recipe and click "Edit Elements" -> Choose "Load Plugins".

Can I customize CSS?

Yes, you can apply CSS on glossary term in article and also on the component view.
But in most case you won't need it because you have some visual selectors for colors, border-radius, shadow, tooltip styles... in component parameters.