Can all types of users (e.g., admin, data scientist ...) create the Glossary, Terms, Category, and Classification? And whether it is possible to make any restrictions for some users for these purposes?
And how can the Bookmarks and Popularity score be created in Atlas?
What you refer to as Bookmarks can potentially be done via Saved Searches (see here), depending on what you want to achieve. As for the popularity score, this could be made a metadata attribute that can be updated by users. There is no automation to derive this score with Atlas out-of-the-box.