I don't keep a lot of books on my Kindle, legacy books or those from Amazon, just because navigating through too many of them is tedious, even using collections.
As for legacy books, the only difference that makes them troublesome appears when you need to transfer your books to a new Kindle, or reload them onto your current Kindle.
In that case, only books downloaded from Amazon will automatically place themselves into the Collections you had put them in.
They do go into them manually just fine, though.
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