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The main reason that ereaders have anything to do with FAT is because of UMS, USB Mass Storage.
This is the system that allows you to plug your ereader into a desktop and see the ereader as a removable disk.
ADE, Adobe Digital Editions expects your device to use UMS.
If you sideload everything using ADB or MTP you might not need UMS.
If you don't use UMS you can use any file system that is supported by your ereader for your content.
You can also get rid of vold, the volume daemon.
If you switch file systems you may have to modify fstab.
My $0.02: UMS, vold, FAT, timestamps in local time all stink.
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