The nationality of the author and the place of business of the internet portal have little to do with the spelling in a book. This is entirely determined by the publisher. If a book is published in Canada, and if the ebook originates with the Canadian publisher, it will almost always be Canadian spelling. (There are a handful of Canadian presses that use US spellings, but by and large, Canadian presses use Canadian spellings.)
Kobo would not change the spelling in an ebook; it's not a simple matter of search-and-replace -- it takes care and attention to do this properly. Plus, Kobo does not have the legal right to alter the text of the book. They're just a bookseller. If anything, Kobo would ask the publisher to provide a "Canadianized" file ... but there's little motivation for them to do so and it's unlikely a US press would agree to do so -- it would be a non-starter.
If a book is sold on Kobo in Canada with US spelling, but that book has actually been published in Canada, two things may have happened: 1) Kobo is selling a version they should not be selling in that region, or 2) the Canadian publisher has print-book rights only, while electronic rights are held by a foreign press, or the author themselves. The latter scenario is rare these days, but does exist.
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