John
The PDF has an index that is hyperlinked. The help file is geared toward context sensitivity.
The help file has an Index tab which is hyperlinked to the rest of the file.

John
The PDF is a proper manual with each section and chapter having its own logic. The help file is a bunch of independent references. The PDF can be read from beginning to end. The help file has no beginning or end.
It would appear the layout of the two documents are the same. Here is TOC and first page of the CHM. Also notice the navigation arrows at the top of the page. Those can step through the CHM one page at a time from the first to the last page.

John
The PDF is printable the help file is not so easy to print out and use as a manual. The PDF can be read on an android device the help file is Windows only.
I have not printed either and do not have an android device. I did search Google for printing CHM and CHM readers for android. There do seem to be solutions for both.
None of this is to be taken as favoring one format over another. They both have their champions. They both contain the same data in the same layout.