How to enable "Allow Remote Automation" in Safari programmatically

It is not possible to toggle the setting using the method you described.

Starting in Safari 11, you can force safaridriver to authenticate by using the --enable command line option. After authenticating, this menu item will be set. This will also cache the authentication for the rest of your login session. Subsequent invocations of safaridriver (say, by the Selenium libraries) will not need further setup.

It can also be done using AppleScript if it is not possible by modifying the plist. To do that, first enable develop from Safari preferences and then choose Allow Remote Automation from the Develop menu.Here is the AppleScript that I wrote to enable Allow Remote Automation (this covers both the steps mentioned above).

tell application "Safari" to activatedelay 2tell application "System Events"    tell application process "Safari"        keystroke "," using command down        set frontmost to true        tell window 1            click button "Advanced" of toolbar 1            delay 2            set theCheckbox to checkbox 4 of group 1 of group 1 of it            tell theCheckbox                if not (its value as boolean) then click theCheckbox            end tell            delay 2            keystroke "w" using command down            delay 2        end tell        tell menu bar item "Develop" of menu bar 1            click            delay 2            click menu item "Allow Remote Automation" of menu 1            delay 2        end tell    end tellend telltell application "Safari" to quit

Note: Here I enabled develop menu from safari preferences only if it is unchecked.

Hope this helps..