I think I understand. Council doesn’t believe you live in the suburb and is trying to control the number of permits due to the local business district.
Still I don’t think they have the right to say no even if there is already a carspace in the building (some families have more than one car). I’m not a real estate specialist but it seems the real estate agent is also restricting your right in regard to obtaining the permit.
Maybe if you go back to council with more evidence of your residence they will come around. Better still send a written complaint and ask for a written answer explaiming why they are refusing. Beaurocrats hate putting anything in writing as they then can’t deny it. It might make them reconsider.