Even if you use "id" in place of "name," it's best to put those anchors
before the header or other element you're linking to, like the guidelines say.
Of course the best way to avoid the styling "quirks" that can occur with MOBIs when linking to your various chapters is to not use url fragments
at all. Instead, break your chapters into individual html files and link directly to the files (with no fragment). That way you don't have to worry about the "quirk" (and you won't need to use "page-break-before: always;").
Footnotes can still be problematic, but as long as you follow the guidelines and put the <a id="foo" /> anchor
before your styled "target," you'll be alright.