Thanks, Kovid, for answering. You are of course a God-like figure for us beginning epub makers! We thank you for your great work.
I'm not quite clear what it means to "flatten CSS" Does it simply mean to move the style definitions from an external CSS file into the HTML file itself? Or does it meant to replacve things like <strong><p class="bodytext"> Hello </p></strong? by something like <p class="strongbodytext">Hellow</p>?
Anyway the big point from your remark is that, as I kind of knew but had stopped thinking about, you can author your EPUB without using Calibre. For instance, write an HTML you're happy with and add that into a new Sigil EPUB and you have an EPUB with the code you might prefer. And I learned a trick for having Sigil split the big HTML into small files so it's all good.
This said, for a beginning EPUB maker, it works fine to just load the HTML or even the RTF into Calibre and let Calibre convert to EPUB and don't freak out over the kind of intricate styling statements that end up in the code. I know YOU know this, Kovid, but I'm just writing this down so I remember it and possibly to be of help to some other noob.
One thing I found I really did need to use Calibre for was that I had a whole website with thirteen separate pages, and it was really easy just to load the index.html into Calibre and it dragged along all the other files and pumped out a usable EPUB, downloadble as issue #14 of my Flurb webzine.
---Rudy Rucker