Use Automator to open app as itself?
Does it have to be Automator? 

I have an app which will take additional parameters at launch, which I do by saving an Applescript as a self-contained App.

The basic config is

do shell script "\"/Applications/NameOfApp.app/Contents/MacOS/NameOfApp\" -param1 -param2 -param3"
quit


Edit - Ah, reading more carefully, nope, that doesn't hide the icon of my applescript whilst it's running, &amp; it will not quit until the launched app is itself first quit… but it wouldn't be confused for the app itself.
They are parent/child processes so will be displayed individually in the Dock.

You may be able to hide it like this question - Hide a running app from Dock?
…which rather makes this answer a bit pointless ;-)