You bring out a good point, and you are not the only one who would like to be in control of how the device behaves.
In fact, most of the activity here is inspired by Amazon's attitude that even though you own the device, they still own the behavior.
For your own case, I would suggest what others seem to like (I don't use this combination myself) -
Manage collections on their PC with Calibre and then use our LibrarianSync add-in to update the Kindle collections to match.
https://www.mobileread.com/forums/forumdisplay.php?f=166
http://calibre-ebook.com/
Also scattered around this forum are add-ins that interface with various on-line file storage services.
That is one way to be sure Amazon isn't data-mining your reading preferences just to improve their bottom line.