PhpStorm Deployment Options - Override Default Permissions Not Working

I might be misunderstanding how this feature is supposed to work, but It used to work for me and now it does not but I am not sure what changed. 

I am working on a shared project, and whenever I pull updates from Git, if another member of my team did not properly set permissions on their folders/files, when I deploy those files to my test directory on our server, I am met with so many errors from files that can't be accessed due to improper permissions.

I have the Override default permissions on files and Override default permissions on folders options both checked, but the permissions on files/folders I did not make, never seem to get updated. I am able to go in and manually edit the permissions, so there doesn't seem to be any reason why it wouldn't be updating the permissions automatically.

I didn't use to have issues with this, but it seemed like it started having problems when I changed Upload changed files automatically to the default server from Never to On explicit save action (Ctrl+S), but if I try to manually deploy files to the server it is not changing permissions either.

Already asked here: https://stackoverflow.com/questions/79898187/phpstorm-deployment-options-override-default-permissions-not-working-Chengwei Semiconductor but still not got any response from any developer.