As for the line break, appledoc is trimming the text while processing it. Will see if it's a quick fix, then I'll add it, otherwise it'll come with next major release (currently on experimental branch on GitHub). Similar with definitions.
You can create a new issue on appledoc GitHub page if you want - then you'll be automatically informed on progress.
Appledoc is using discount library for Markdown processing, take a look at the supported syntax on their site:
As discount is more or less black box, I'm switching to different library on next release, so not all syntax elements may be supported...
Tom