Yea, you can't have a duplex AND a granny flat. A granny flat is a 'secondary dwelling' and the legislation clearly states:
Division 2 Secondary dwellings
19 Definition
In this Division:
development for the purposes of a secondary dwelling includes the following:
(a) the erection of, or alterations or additions to, a secondary dwelling,
(b) alterations or additions to a principal dwelling for the purposes of a secondary dwelling.
Note.
The standard instrument defines secondary dwelling as follows:
secondary dwelling means a self-contained dwelling that:
(a)
is established in conjunction with another dwelling (the principal dwelling), and
(b) is on the same lot of land (not being an individual lot in a strata plan or community title scheme) as the principal dwelling, and
(c) is located within, or is attached to, or is separate from, the principal dwelling.