Can't the term "Australia" just refer to the place on the globe? Like if someone was telling me what Antarctica looked like 50,000 years ago, I wouldn't tell them that Antarctica didn't exist back then. I'd know what they meant.

"Australia's history" was a poor choice of phrase exactly because of that ambiguity. In fact it was explicitly referring to the period since 1901, which very few people would consider to be the start of "Australia's history".