I think that markdown is either one of those things you love or hate. I love the fact that a enter is not considered a break, personally. I can format my source in any manner that I fashion, and know that the final formatting of it will be based on the markup, not the actual formatting of the source. That said, your problems are easily solved - two or more spaces at the end of the line force line breaks, which I don't personally think is too onerous.
As far as Gitbook, I found it the same as a lot of things built on Chromium- not ready for prime time. I now use a combination of sublime text and
notebooks for my writing projects. I tried to use Scrivener, and really want to use it, but it's just not compatible enough with syncing services and plain text for me to use it.
But as a platform, I think they made the right choice in separating the publishing from the actual payments. I really like Gumroad, and having them work more on integration made me like the platform (if not the tools) more, rather than less.