It's not a bug because it's all about priority - css is cascading, and the 'remove blank lines' feature is a big giant hammer that takes highest priority the way it inserts itself into the css. In order for extra css to work after you've used that feature you need to define extra_css in a way that takes HIGHER priority. That can only be done by reviewing the html/css manually so you know what classes to override.
I think people have explained this to you in several of the half dozen threads you've got going on this same topic.
If you want fine grained control, keep a backup of your original, and just use extra css during conversion. If you want to tweak something, restore your original, tweak the extra css, re-convert. Avoid the remove blank lines feature - it was designed for users who wanted brain dead simple formatting.