Just chiming in to say I'm having this on a PW6 as well. Adding SEARCH_LIBRARY_PATH = "/mnt/us" to defaults.custom.lua had no effect (in fact, that field doesn't even show up in the KOReader advanced options even when I set it). The documents sideload fine -- no changes to the path where things upload. In my case, the calibre metadata thinks they all live at "documents/whateverbook.epub," and that's what both Calibre (and OpenMTP) see them as relative to the root that they mount, but this fails from KOReader's perspective.
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