Jon, a lot of what you're putting forward as "best practice" is really just your preference. Many people, for example, prefer generous margins and find little-or-no margin very hard on the eyes. Justified text is preferred by some, not by others. Justified text on a small device looks awful. (Although some of the newer display modes that shorten lines that would otherwise be hideously spaced out is not a bad compromise.) The best option, where possible, is to leave it for the end-user to be able to choose justified-unjustified. Spaces around em-dashes are not necessarily a mistake; it's a matter of preference. I don't use that method myself, but one good reason for doing it is that it ensures a line can break at a dash, rather than having the dash bind two words together.
The section break is practically an art in itself. I have begun using single-line section breaks, with style set for additional spacing above and below, and a simple typographical centered (centered!) marker such as * * * or o0o or ~~~. But there is no one "correct" way to do it.
Don't even get me started on ellipses.
On your statement "Don't use Word," I say, not true. It's all well and good to say build the formatting from ground up in Sigil or whatever, and that's fine if you have endless time. But most authors want to get back to their writing. The fact is, you can build perfectly good ebooks using Word (the Smashwords Style Guide offers many useful tips), if you are careful with styles and are willing to tweak a little as needed. So the CSS isn't quite as clean as you would like. It still works, and if done carefully works very well.
But I still wish Calibre would offer the option, which Kovid indicated wouldn't be hard, to add a line ensuring that centered text would truly be centered. He doesn't want to, and that's his right. But I think it would be an improvement that people would appreciate.