PDF preserves layout whereas html doesn't (generally, although it can preserve layout somewhat if you specify one font, fix font sizes, and fix all dimensions), but that's a
negative for PDFs.
Different displays have different resolutions and different dimensions. That makes fixed layouts obnoxious to read on e-readers. The most obvious example of how fixed formatting is an abomination is a PDF on an ebook reader.
There is one reigning reason for having a fixed page layout: ability to cite pages, e.g. for academic citations.
There is no need to cite pages for works that have good digital versions, other than antiquated citation requirements (e.g. MLA/CMS). Ebook readers have text search. Cite a digital form of the work, and anyone with that work in digital form can find it... an exception being OCR'd pdfs and ebooks converted from PDFs, because OCR often screws up line breaks or has other errors that make searching unreliable.
For less-granular searching, there's section, table, and image numbering/labeling. Again, fixed layout is not required to make content searchable.