(A) before Australia was Australia, it was the antipodes
CORRECT
(B) before there was Australia, it was the antipodes
what does "it" refer to? with 'before there was Australia' the sentence refers to the time before Australia, not the location
(C) it was the antipodes that was Australia
Confusing because 'it' seems to England or the people - either way logically wrong.
(D) Australia was what was the antipodes
"was what was" is incorrect = Australia was the antipodes is better
(E) Australia was what had been known as the antipodes
There is no reason for the past perfect 'had been known'
___________

Choice A is best, for A alone makes clear that the land now known as Australia was considered the antipodes before it was developed. In B, it has no logical referent, because the previous clause describes a time when there was no Australia. Nor does it have a referent in C: substituting Australia for it produces a nonsensical statement. D is wordy, with the unnecessary what was, and imprecise in suggesting that Australia was considered the antipodes after it became Australia. E similarly distorts the original meaning, and the past perfect had been is inconsistent with the past tense used to establish a time frame for the rest of the sentence. Hence, A is the answer.