Apparently if it's not modified in the Setup, it doesn't get saved and MODX falls back to a default. Line 76 of /manager/controllers/default/workspaces/index.class.php:
'new_folder_permissions' => $this->modx->getOption('new_folder_permissions',null,0775),
And for files, line 359 of core/model/modx/modfilehandler.class.php:
if (empty($mode)) $mode = $this->fileHandler->context->getOption('new_file_permissions', '0644', $this->fileHandler->config);
So to change it, create two new System Settings, new_folder_permissions and new_file_permissions. It looks like you should be able to add new_file_permissions to a Media Source's properties as well, and possibly also new_folder_permissions.