Two things are getting mixed up. Driving License and driving permit are not the same. Heck, is there really anything called Driving Permit??
Driving license gives you the authority to drive a kind of vehicle clearly mentioned in the license. It is issued for driving that particular kind of vehicle, i.e. with a driving license authorizing you to ride "MotorCycles with gear" does not authorize you to drive "Light Motor Vehicles".
Permit is issued by local governing body authorizing you to reach and roam around in certain places mentioned in the permit by whatever modes of transport, be it walking, biking, riding or driving.
So, you see, Indian Government can issue you a Driving License to drive in India but can't issue a permit to roam around in Nepal. That permit/visa you will have to take from Nepal Government/Competent Authority.
AFAIK upon entering Nepal you will be issued a temporary registration number for your vehicle (maybe a temp DL too, not sure). And as Shamik has pointed out, if you show an Australian Passport along with an Indian DL it will only complicate the matter. Best is to contact the Nepal Consulate and sort out all things with them, if possible in writing.
Good Luck.