I do understand your point but you could also argue that's when you need padding the most because it becomes infinitely harder to visually parse the raw text.
I like your idea for giving people the option though.
> Document Node is not just a pure Markdown editor, it has a beautiful HTML5 preview area, where you can see your tables in a perfect format.
Document Node is a nicely polished product but it's worth remembering that the point of markdown is that it's still readable without needing a viewer that supports rich formatting. For example it should be just as readable in the terminal as it is in a HTML5 container (this is one of the reasons I don't really like tables in markdown but that ship has already sailed). Unfortunately not everyone will be using Document Node to view their markdown.