The Kindle apps are replacements for the MobiPocket apps, and by making them distinct Amazon was able to ditch a lot of old pocketable devices. This was a plus because they could target larger screens exclusively. It did leave older devices in the lurch though.
They were perhaps brave when first introducing the iThing apps, because at that time they were heavily discounting ebooks and many comenters thought device sales were subsidizing ebook sales. I say perhaps because I was never convinced they were loosing money overall on ebooks.
B&N has cloned the Amazon approach, they also had eReader apps that are not the same as B&N apps. They do still support eReader DRMed ebooks (I think), but that is partially due to their DRM scheme being password based.
Kobo has a distinct approach to apps, which do not read the same ebook files as used on EInk readers but rather a Kobo specific "mobile" format. In a sense they are the last holdout of the old way of doing apps.
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