Maybe we are arguing the same thing.
The script is changing the permissions of all files and directories under ~openhab whether you created the user yourself or it was created as part of the install. It also changes all the permissions of any files you may happen to add to that user’s folder.
On my install where I let apt-get create the openhab user it appears to put ~openhab in /var/lib/openhab so it actually has the Designer workspace, zwave, and persistence directories in it. I wonder if the setpermissions.sh script assumes this is the case for all installs and is infact missing some files it should be changing permissions on for users like you who created their own openhab user. The script does not appear to look for or change anything in /var/lib/openhab directly and I wonder if that is the real intent.
At the end of the day, for me at least, if I want to run ssh using keys instead of password from openHAB I have to put the ssh keys in ~openhab/.ssh and the permissions on those key files must be user read/write only. The setpermissions.sh script breaks this for me and I wonder if it breaks it for others without their realizing it.