I don't think it's a bug is it? Android works on a sandbox basis does it Not, so that when we save files on a pc it goes to the media folder in my docs, android does similar. I know that if you try and load anything, it first checks the sandbox folder for the file, then the root - so in pc terms it will load the copy in my docs media before the main root of the app. So in that sense, scanning the folder also looks for the sand box folders first and scans them. I think on PC that's why the RAW commands were added, but I believe on android you cannot scan outside this unless the device is rooted, or has special permissions.
So i would day it probably is by design, it's just not a perfect design. The zip idea is clever though, but will double your storage as likewise you can't manually delete that zip from agk on android.....you could only delete a my docs saved copy of it, if that makes sense.