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Yes, they'll show up as personal documents. Only "Send to Kindle" will be backed up and sync using Amazon's cloud.
There's a Calibre annotations plugin that works with the "My Clippings.txt" on Kindle e-ink readers. I'm not sure but I believe the plugin only does a one-way sync from Kindle to Calibre. @davidfor can correct me on this. Caveat, while annotations created on the Kindle for Android or iOS apps are synced to Kindle ereaders (.mbp1), they don't get exported to "My Clippings.txt".
I hear you about the crappy native collection management. I purchased extra Kindles just so I have jailbroken backups that work with LibrarianSync + Kindle Collections.
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