What is the difference between Bookmarks and Table of Contents in a PDF?
Different programs can use different terms. "Bookmarks" can be added in PDFpen and are essentially placeholders which appear before the Table of Contents in the Sidebar so you can quickly reference a specific saved page aside from the Table of Contents. Bookmarks are named in PDFpen and PDFpenPro as "Page [x]" where x is a page number by default.
Editing the bookmark name is an advanced feature found in PDFpenPro. PDFpenPro allows you to add and edit Bookmarks as well as Tables of Contents. Table of Contents in PDFpenPro are an aside to the document and link to any page you want (e.g. an annotation).
PDFpen (where PDFpen refers to all versions of products in the PDFpen family) uses a different term, "Table of Contents," then Adobe products, which use the term "Bookmarks," for the same feature. Both Table of Contents (PDFpen/Pro) and Bookmarks (Adobe) are links to content, most often within the same document, which are stored within the document and are portable across computers. In the PDF specification, they are called "outlines," which is an overly loaded term neither product uses. Table of Contents from PDFpen/Pro is viewed as Bookmarks in the Adobe products, and vice-versa.
To make matters worse, Preview uses BOTH terms, each for different things. The "Table of Contents" in Preview is the same as the Table of Contents in PDFpen/Pro and Bookmarks in the Adobe products. However, "Bookmarks" in Preview are specific to the Preview application. Bookmarks added in Preview is not the same, and do not appear in the Adobe products. Similarly, bookmarks from Preview do not show in PDFpen/Pro or other PDF applications either.