I have, indeed, noticed, that what PCG uses as "states" for Malta does not correspond to any administrative units but is purely artifical. It would make more sense to use either the five regions or the six (statistical) districts as "states". (In both cases Comino would be together with Gozo then.) When it comes to Comino, indeed this is part of the local council of Ghajnsielem (Gozo).
The island on which Fort Manoel stands is part of the local council of Gzira.
I don't know whether it would be possible to keep the three "states" and nevertheless add the local councils as "counties" - in this case probably one would have to define Ghajnsielem as the part on Gozo only and attribute only one 3rd level unit to Comino, e.g. called "Ghajnsielem (Comino)" or, ideally, to replace the three "states" with the five regions and then add the local councils as "counties"? (I assume the case of Gzira should not be a problem, as there are other instances where administrative units consist of several parts not physically linked to each other, should it?)
It would be really great if this could be done.