Listen to the insurer as they are the ones who can make your life a misery should you need to make a claim. You don't want them wiping you because you listened to an agent who got it wrong. If you find an insurer who allows you to rent a granny flat separately that is not legal head height make sure you get it in writing and keep that document very safe.
We have friends who used to live in our street in a three bedroom house that had laundry, study, garage, living room and a store room downstairs. Had they stayed, and not added the fourth bedroom upstairs, the older kids would by now probably have moved to the two rooms downstairs.
The head height is short of legal by about ten centimetres. It feels a little low, but certainly is livable. They used the living room downstairs all the time as a family TV room. However, to rent such a space saparately would (in my opinion) be illegal. The "bedrooms" are called "store rooms" they are not considered legally to be a bedroom because they don't have legal head height.
They had tenants who were two families..... two sisters, each with a few children rented the house as a whole and one sister and her children slept downstairs (kitchen was upstairs) while the other sister and her children slept upstairs.
I think this was acceptable only because it was rented as ONE HOUSE. I don't think the agent would have been able to rent the downstairs separately due to the head height, even if it had a kitchen.
Legal head height is worth money. A house short of legal will always (generally) get less because anyone wanting to build into the downstairs is up for around $30K or whatever it is to raise or dig out.