Disable Pop-Up Blocker in Safari. This disables the pop-up blocker selection in Safari under Security > Web Content.
To turn Pop-Up Blocker back ON, where command ends "...WebKit2JavaScriptCanOpenWindowsAutomatically" replace the ending "1" with a "0".
Tested on OS X 10.11 and macOS Sierra 10.12 in a MDM environment. Please note that usage in other than a managed environment is not needed.