When Judge Flannery talks about 'representative counts' and 'parts of a course of conduct' he's referring to the fact that there were more sexual assaults of the particular child (ie, his 11 year old female victim) by AJ than the charges brought against him, is all I can gather; but I'm no lawyer.
Australian Government, Australian Law Reform Commission, Section 25, Sexual Offences, Persistent sexual abuse of a child:
"For example, in the revised South Australian provision, reference to ‘persistent sexual abuse of a child’ was replaced with ‘persistent sexual exploitation of a child’. The offence now focuses on acts of sexual exploitation that comprise a
course of conduct, rather than requiring a series of separate particularised offences."
https://www.alrc.gov.au/publications/25. Sexual Offences/persistent-sexual-abuse-child#_ftn125
Crimes Act 1900 (NSW), Section 66EA, 'Persistent sexual abuse of a child':
"(1)
A person who, on 3 or more separate occasions occurring on separate days during any period, engages in conduct in relation to a particular child that constitutes a sexual offence is liable to imprisonment for 25 years.
(2) It is immaterial whether or not the conduct is of the same nature, or constitutes the same offence, on each occasion.
(3) It is immaterial that the conduct on any of those occasions occurred outside New South Wales, so long as the conduct on at least one of those occasions occurred in New South Wales.
(4) In proceedings for an offence against this section, it is not necessary to specify or to prove the dates or exact circumstances of the alleged occasions on which the conduct constituting the offence occurred."
http://www.austlii.edu.au/au/legis/nsw/consol_act/ca190082/s66ea.html