By "command line option", do you want to add more items to the drop down menu when you right-click on a dock icon?
(I'm not quite sure what you mean by that!)
Can you give us an example or two of what you would like to do?
I doubt that an app update will have any affect on an icon in the dock. Of course, if you use particular options that might not continue to be allowed, because of an update to an app, that would be something that you would need to question the app developer, or online support forums for that app.