The Regulation is primary legislation with which everyone must comply. By definition, if one complies with an AMC, which is secondary legislation, one is also complying with the Regulation. There may be more than one acceptable means of complying with any specific implementing rule, in which case one may choose to comply with any of the Alternative Means of Compliance (AltMoC) that are available. In the case under discussion, the Regulation requires "refresher training of at least 1 hour of total flight time with a flight instructor (FI) or a class rating instructor (CRI)" and the UK AltMoC does not conflict with that requirement. However, one may also comply with the implementing without complying with the AltMoC - completing a ten minute flight with each of 6 instructors will comply with the Regulation but not with the UK AltMoC. It is not a matter of choosing between the implementing rule and an acceptable means of compliance but of choosing between alternative means of complying with the rule. Clearly, if there is only one acceptable means of compliance, that is the only means by which one may comply with the rule unless one notifies an alternative acceptable means to the competent authority.
An important fact to bear in mind is that, under EU law, AMCs (or AltMoCs) cannot create additional obligations to the Regulation, so the UK CAA cannot, at present, enforce its limit of 3 flights or one flight instructor as these are additional obligations to those required by primary legislation. After 31 Dec, however, who knows?