With most dark themes the main font in markdown preview window is barely visible: light on white background. This has been fixed in Atom 0.190.0 with One themes, so apparently it's a theme's job to define appearance of such things. Example here.
Making it adapt to current syntax color scheme would be perfect. However, adapting themes to all the packages out there will be tedious in the long run. Perhaps folks of Atom could outline a common convention for styling such panes. I haven't yet found anyone bringing up that issue.