My last commit to the PR includes a fix by delaying setting permission to all files, not just to directories, in .extractall().

It might be better to catch the problem during .add instead, preventing tarring multiple copies, but I found subtle difficulties with that approach.  (Do we have a foolproof way to establish that a second addition is a duplicate?  What if the filename and path is the same, but the file has been changed since last time it was added to the tar?)
 
This solution uses code that's already present.