The use case I was thinking of when making that decision was having the default bootstrap theme in the header, then allowing the user to specify an alternate theme with the markdown_css argument.  I see the point about overriding the defaults though.  Maybe the solution is to use the skip_style markdownHTMLOption on whether to include the default styles or not, with the default styles being included before the header, and change the markdown_css argument to be included below the header, then you could override the default styles in both the header an in an external css.  If you don't need the default styles at all you can just use the skip_style option.  The only change given this scenario would be to add an additional #!default_markdown_css# variable before the header, an include the default stylesheet there unless skip_style is on.  Let me know what you guys think.