I found my issue and it was actually caused by running as sudo vs the user. When I was executing the AppleScript in the script editor it was running as my user account and editing the com.apple.dock.plist in my /User/.... folder. This has the intended behaviour of editing my dock. When I ran the same code, osascript or bash directly, as sudo it did not edit the com.apple.dock.plist in either my user directory or the system directory /Library/Preferences/.

I am now trying to use PlistBuddy to explicitly edit the file that I want, taking some time to learn today