Probably the App Store version. I can’t extract this stuff to my home folder - this is all huge archives that live on an external drive.
The request it’s giving though doesn’t seem to be the one from the bug report. I have that preference set, and it knows where I want the extraction when the window pops up - but it keeps acting like it doesn’t have permission to put files into that folder.
Running the following command in Terminal worked for me though you need to wait a couple minutes to takes effect. Next time you double clic on a compressed file to extract it, The Unarchiver will show a prompt as if it was running for the first time, and will decompress the file too.