We do not impose any layout preferences on anyone.
We generate ebooks with our layout preferences. Our layout preferences are based on the idea that for an in-progress ebook, layout is not as important as finishing the book.
Now, for a finished print book, layout is important. But the last thing in the world that we would want to do is re-create InDesign, in a browser, badly. So, instead, we offer a free InDesign export, so you or your book designer can do layout in actual InDesign, not in "poor man's InDesign".
Our InDesign export feature is here: https://leanpub.com/YOURBOOK/in_design
The reason most of our layout settings are global is because we don't want you wasting your time doing layout in your manuscript when writing.
Layout should be done via global options which apply to your whole book. The options we currently support are at: https://leanpub.com/YOURBOOK/settings/theme. Here is more information about Book Themes: http://help.leanpub.com/en/articles/3691789-what-are-the-settings-for-each-of-the-different-book-themes.
The way to have the most control on that page is to choose Custom formatting.
This is our position, both in Leanpub Flavoured Markdown (our current default for book writing which is specified fully here: https://leanpub.com/help/manual) and in Markua (which you can read the spec for here: https://leanpub.com/markua/read).
Note that Markua is more fully specified than implemented. We are a bootstrapped startup, and we have limited resources. We expect that Markua will be fully-implemented this year. The current status of everything we still need to build in our Markua implementation is listed here: https://leanpub.com/markua/read#leanpub-auto-todo-in-leanpub
That said, even when our Markua support is 100% done, Leanpub will not be "InDesign in a browser". When our Markua support is 100% done, Leanpub's layout options will be basically as limited as they currently are.
Over time, we may add more global layout settings for things. We already support many basic global layout settings, such as line spacing, font size, endnote location, body font, code font, title font, code font size, page size, paragraph indenting, table of contents levels, section numbering, scene breaks, table width, caption styling, etc. All of these can be individually customized via our Custom theme. So, chances are, things like spacing before lists, spacing after lists, font size in asides, etc., may be things which are also customizable via the Custom theme.
But, to be frank, the same person who would build those changes is also the same person who is finishing the Markua support. So, chances are, there will be no more layout customization options in Leanpub until Markua is 100% supported, which is at least a few months out...