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You can buy a Kindle DXG and never buy a book from Amazon. There are plenty of folks who do that. It has a great 9.7 inch Pearl Screen and is easy to take notes on. It is not the best reader for PDF's. It works well but you cannot manipulate them easily and there is no automatic reflow.
The Sony 950 might work for you. It has a 7 inch screen and is one of the best for reading PDF's. IT ahs the pearl screen but I don't believe that it is linux based. You can take notes on it pretty easily and it has PDF reflow.
I realize that neither of these devices are on your list but they are well known, well tested devices that work for a fair number of people. You don't have to buy books from any store to use any e-reader, the DXG and 950 are no exception. You can sideload free content easily enough.
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