Hey Adam, I would have loved to be able to work through each of these issues in turn to get it all sorted out. I've made changes to the way we handle the GitHub generated HTML and provided a page that allows you to test how it all goes so you can either work around issues your end or yell at us with specific examples we can debug against our end. I'm also happy to talk about our editors diving in constantly to help editing typos but I can't help with markdown tables because we use the HTML that GitHub sends us based on the README file. There's tons of things that can be added to this system but I'd prefer to focus on things like the WYSIWYG issues you mentioned. It's a very simple system to provide a very simple and limited solution. The more people who use it, and help us iron out the niggles and help us work through what's important and what's nice, the more able we are to dedicate resources to it.
cheers Chris Maunder