Instead of converting everything, I recommend you use the
Modify ePub plugin which comes with numerous fascinating features for doing an in-place modification of an ePub WITHOUT resorting to a full conversion. Conversions do all kinds of changes, not al of which you may like.
Specifically, the "append extra css" setting.
And Modify ePub settings for css are drawn from the defaults, not the saved conversion settings, if I understand it correctly.