Making file associations launch a certain extension, but with a console program?
Yes, you need to wrap the console program in something that turns it into a Mac app, Automator being the easiest way.

Select 'New' in Automator's File menu and create an application. Application's in Automator automatically receive the selected files and folders.

You just need a single Automator action, "Run Shell Script". The body of the action is the console command. You then set it to pass input as arguments.

Once you save it you can use it in an "Open With" dialog but you will have to browse to it using the "Other" selection.