Nope. macOS aliases suck. It’s a binary unmodifiable file that can only point to a file, it can’t specify anything additional.

Is there a reason you can't add a script to your path and alias that?

    #!/usr/bin/env bash
    my-command --flag --another-flag $@

As far as I know, you can’t get an executable script like that to act like an app that’s launchable when double clicked from Finder or clicked the Dock. Even though it’s executable.

I just tried it, seems to work! Make your script with custom options, mark it as executable, make an alias for it within finder, and drag that into your dock.

You can create a folder with a '.app' extension and put the script in there. Just make sure the script is executable with chmod and remove the '.sh' extension.

Bash aliases (or whatever shell you are using) work exactly the same.