With harmonised EN standards with presumption of conformity, there is a shifting of the burden of proof. If the standards are applied, it is assumed that a manufacturer will also meet the specific requirements of the directives. The regulatory authorities would therefore need to prove that a manufacturer did not meet the legal requirements.
However, should you deviate from the harmonised standards, you yourself must demonstrate how you have met the essential safety requirements. This is generally done via the hazard analysis.
In practice one would endeavour to apply the harmonised standards, unless the products were highly innovative and no harmonised standards existed yet.
The standards for which this "presumption effect” applies can be researched in the Official Journal of the EU.