Does choosing module A by itself give the product presumption of conformity?
No.
Module A is only a conformity-assessment route. Presumption of conformity comes from the Article 27 tools, such as harmonised standards, common specifications, or qualifying European cybersecurity certification schemes, to the extent they cover the relevant requirements. If the manufacturer does not use those means, it may still use module A where the product is eligible, but it must explain in the technical documentation how compliance is reached otherwise.
Article 27(1), (5) and (8), Annex VII point (5)
sections 4.1.7 and 6.6