I think the experiment that needs to be done is to compare the file which is downloaded from personal documents service with the one you sideload. PDS does muck with the metadata and it may be doing something with the cover image as well. Calibre (or KindleDump) might be able to show what is different.
Another idea: save off a copy of the downloaded file, remove the downloaded file, and then side load the copy. Does thumbnail show up? I
Kindle for Android shows cover thumbnails consistently for me, and even on my Paperwhite and Kindle Touch, a few items from PDS have thumbnails. Sideloaded content always has them (when there is a cover image in the file)
I believe thumbnails are generated on the device so it may be that PDS has done something that makes the thumbnail generation fail.
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