1. Leaves all kinds of css, image file, which might be hundreds for each saved page. SingleFile saves everything in a convenient, working, single file. 2. is not really saving all the info.
I got burned when I was using Mozilla/Internet Explorer to save mhtml files, which ended up not being supported anymore. Additionally, turns out, they were saving the original versions of pages, without the Javascript changes, meaning that all the opened threads of comments I wanted to save were never saved! Never again!