You'd be better off asking the Shopify community, or somewhere like an Aus markeplace seller facebook groups, as you're likely to reach more sellers using multiple platforms and have encountered - then implemented solutions for - problems like this. I use Shopify but do my accounting pretty much manually, so can't help with that, but I suspect since there is literally nothing on eBay AU that distinguishes or extracts GST from sale prices, you'd most likely need to use a third-party accounting program that sets up a specific rule for eBay revenue.