Well, there is some work being done on Sigil, at the moment, it just isn't ready yet. Also, there is an experimental EPUB3 output plugin, which I believe fixes the packaging as Sigil already forgives the presence of multimedia.
EPUB3 is still treated with much skepticism outside the limited field of fixed-format and/or multimedia, so it is difficult to get people willing to work on support.
calibre works just fine, at least, the
editor component will handle EPUB3 just fine depending on how you use it. The important thing to realize is that it is no different than Sigil in editing the raw HTML, although it has a slightly different set of tools.
It is true that calibre
conversion will produce blended (think food processor) ebooks, meant for end-users. And often these will be rejected by stores.
The editor is a recent creation, far more recent than the lore that says stores reject anything that calibre touched.
calibre's
Edit Book might be worth taking a look at, you may wish to add it to your tools(, or you might decide you prefer Sigil).
Glad you found something that helps you
although it is worth keeping in mind that learning the ins and outs of HTML+CSS (at least, the subset used in EPUB) is a useful long-term goal for anyone who will be working in the ebook field. It can save you a lot of bother in figuring out why something doesn't work.
You don't have to be an expert, but having familiarity can save time in the end.