[DiapDealer]

Not much has really changed. When it comes to major reading devices/apps, pop-up notes are really only viable using the iBooks app or the Kindle PaperWhite. And even then, you would basically need two different versions (code-wise) of the book to make it work on both.

As far as creating/editing epub3s for iBooks, I thought Apple had their own program for doing so.

Also, the editor in calibre doesn't try to fix things for you behind the scenes (like Sigil does), so while it’s not really indended to be an epub 3 editor, I see no reason why it wouldn't save valid epub3/html5 code. Provided, of course, that you didn't use any automated beautifying/fixing features.