I got it working with this:

open -b com.adobe.AfterEffects --args /Users/[user]/Desktop/[folder]/file.aep

seems all I had to do was get rid of the r flag.

Good luck!

This is actually documented here

You should now be able to use DoScriptFile (instead of DoScript) with Applescript. Something like:

tell application "Adobe After Effects CS6"
  DoScriptFile path/to/file.jsx
end tell

you can also call a specific function using external parameters by mixing this method with the one mentioned by MentalFish

• make an applescript [in this case called ASfile.scpt]:

  on run argv
      set SomeName to (POSIX file (item 1 of argv))
      tell application "Adobe After Effects CS6"
          DoScriptFile SomeName
          DoScript item 2 of argv
     end tell
  end run
  

• from python and assuming you have a 64bit machine you can call:

  ae = subprocess.call( arch -x86_64 osascript /AppleScriptLocation/ASfile.scpt %s/SomeScript.jsx "SomeFunction( %s )"  %( ScriptsFolder, ParameterFromPython),shell=True)
  

Apparently AE on Mac does not support command line execution of scripts: http://www.aenhancers.com/viewtopic.php?f=8&t=1903

This works, create an AppleScript that tells AE to run the script via the DoScript command:

set test to (POSIX file ("/Users/username/Desktop/test.jsx"))
tell application "Adobe After Effects CSYourVersionNumber"
    DoScript test
end tell

... and run the script via the command line as such (to run it in 32-bit mode):

arch -i386 osascript test.applescript

If you want to pass in the parameter of what script to launch you can do it like this:

on run argv
    set test to (POSIX file (item 1 of argv))
    tell application "Adobe After Effects CSYourVersionNumber"
        DoScript test
    end tell 
end run

Run the script and pass in the path to the jsx file:

arch -i386 osascript test.applescript /Users/username/Desktop/test.jsx

you could place it in the startup folder (I use windows, the folder in win is Adobe After Effects CS4/Support Files/Scripts/Startup). Scripts in that folder are executed upon AfterEffects booting up.

Might be helpful?

I would like to throw in here, some answers where great though possibly outdated. This code:

on run argv
    tell application "Adobe After Effects CC 2018"
        DoScriptFile item 1 of argv
    end tell
end run

For the applescript file works, the POSIX code does not. Then running it in the terminal for Mojave works like this:

osascript AppleScriptAETest.scpt "/Users/.../Your/file/here.jsx"

This works best for me.