I'd be worried. If the landlord has refused to allow you to pay the outstanding rates by using your rent payments then I'd refuse to move in.
You will be liable for the outstanding rates. You could choose to pay the outstanding rates if the place is good enough. I would expect the landlord to ignore the issue if you move in, and to leave it entirely between you and the rates office.
What proportion is the rent to the rates? Would rates for the year be one months rent?, or three? I would calculate the total cost of renting for two years, or three years etc... and work out the overall percentage change if you pay the outstanding rates, compared to if you don't.
You could also check with your insurance company if any certs will be required, or alarm systems, (monitored perhaps).. if so the cost of these should be considered.