WA has an administrative tribunal now called SAT. Apart from your accountants fee for coming up with your interpretation of the law I dont think there would be any other costs if you appeal. In the old days it went through the court system which was very expensive.
Im also in WA and after speaking with OSR they confirm that if properties held in different trusts then land tax is treated separate for each trusts. ie not combined saving lots of land tax.
Are all your properties held in one trust? If so why? Is there any disadvantage Im not seeing in having multiple trusts?