It all comes down to semantics - the difference between EASA's "issued or recognised by a Member State in accordance with the JAA requirements and procedures" and Whopity's "maintained in accordance with JAR-FCL". The assumption seems to be that the two phrases mean the same thing and that a licence that is maintained in accordance with JAR-FCL is recognised in accordance with JAA requirements and procedures. I am far from convinced that this is a valid assumption and, like so much of the EU's badly drafted and confusing law, will only be resolved if/when tested in the ECJ.
Consider this, however - Paragraph 2 of Article 4 makes it a legal requirement for the holders of, for example, UK national licences to have them converted by the CAA to JAA licences by 8 April 2012 (i.e. if any holder has not had their licence converted by that date they and/or the CAA are guilty of a breach of EU law). However, the cover regulation does not take effect itself until 8 April 2012 and so, at the time the offence was committed (before 8 April 2012), it was not an offence because the law did not exist. The ultimate in retrospective legislation (and bureaucratic incompetence).