The meaning of the two sentences is the same, it's just the focus of the sentence that changes.
In the sentence, "There are many plains in Australia." the focus is on "plains". You would want to use this structure if you are writing about plains.
However, if you are writing about Australia, it would be preferable to use the sentence, "Australia has many plains." because it focuses on Australia instead.
So, the general rule you want to follow is to use the version of the sentence that properly highlights the subject you want to focus on.