We get this every so often from authors whose accountants are so focused on the details that the accountants miss the big picture.
Here's the version for EU authors concerned about VAT:
http://help.leanpub.com/en/articles/917414-i-have-a-business-and-my-accountant-says-that-i-need-to-collect-and-remit-vat-on-my-ebook-sales
So, the right way to think about this is:
We're a publisher.
We sell books via our online store and via Amazon.
We pay royalties to our authors.
The authors are responsible for declaring the income and being taxed correctly, etc.
That list may look obvious, and like I'm being rude, since you already know that. But the important point is what is not on the list: anything about GST or VAT.
For our storefront sales, collecting and remitting tax is our job, not yours. For Amazon sales, it's Amazon's, not yours.
Your accountant would presumably not tell you contact Amazon with the information you provided, since it wouldn't make sense. It doesn't make sense for us either :)
So, in terms of your accountant's question: you're receiving royalty income from a publisher as an author, not running an online store and collecting and remitting tax yourself. Just declare your royalty income and pay your income taxes accordingly.
This is part of the value of using Leanpub, instead of running your own store -- many aspects of running a business are inherently annoying and expensive :)
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