PDF reader for Mac that handles bookmarks well I have a couple of PDFs that are composed of scanned images of books. So there is no table of contents for jumping directly to the chapters. As a workaround I bookmark the page where a chapter starts, and use the list of bookmarks as a sort of index.

The problem with Mac Preview is that it doesn't allow to rename the bookmarks and by default all the bookmarks have the same name, so I can't tell which bookmark corresponds to which chapter.

As a alternative to Preview I started using Skim, which is very nice and covers all the features I want but Skim handles bookmarks weirdly. All the bookmarks from every single PDF appear together in the Bookmarks menu (regardless of which PDF is open) and I have to manually make bookmark folders for grouping the bookmarks by PDF's which is tedious and also simple drag and drop doesn't work somehow (turns all the bookmarks into the same bookmark).

I am looking for a alternative PDF Reader that can at least handle bookmarks in a normal fashion. Also if it can embed the bookmarks and highlights and notes into the pdf itself, so that when I transfer it to my other devices these bookmarks and annotations remain.
PDFpen allows editing bookmarks.

PDFpenPro allows editing and creating bookmarks, organising bookmarks, and so on.

They are actually marketed as PDF editors, not just readers.

Both allow embedding all annotations into the document itself.