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As a European, I can't say about Australian GST, but Amazon.com does charge VAT on Kindle books. It's just that on Amazon, the VAT is already included in the price displayed to you and charged from you when you're logged in.
Kobo on the other hand displays me a "base price" and adds the Estonian VAT (20% on ebooks) on the actual purchase page to get the final price. (I think Kobo's price display depends on the country; my German and French friends says that they see the final price in euros already on the book page and it doesn't change between the book page and purchase page, while I see the price in USD instead of euros both on the book page and purchase page and the VAT is added to the initially displayed price.)
BooksOnBoard, as far as I can tell, does not add local VAT at least for me. I don't know whether they do it for other countries.
So based on my experiences, I'd say that it's likely the South African company (not PayPal) that charges GST and it's equally likely, at least in theory, that they pay it on to whatever authority in Australia collects GST; at least I think this is what the companies that do charge local taxes from foreign customers are supposed to do with the collected extra tax money.
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