I suspect that the change to MTP is intended to "modernize" access to the Kindle over USB by making it work like a connected Android device, while at the same time reducing potential hacking vulnerabilities by eliminating unfettered access to the raw disk partition.
It could also be a step toward eliminating access to content downloaded from Amazon's servers. Doing that, combined with further reducing access to download-and-transfer via USB, would better lock down Amazon's DRM.
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