I think you can do this by right-clicking on the instance and choosing "editable children", so you can get inside the instance to find the Area2D and make the signal connection.
Alternatively, you could create a new signal inside a script on the root of the scene, and in that script you also connect the Area2D's body_entered signal to some code that emits the new signal. Since that new signal is on the parent/root of that scene, it will show up in the signals available for each instance of the scene you add elsewhere. If you do this, you can also give your new signal a more meaningful/descriptive name, for improved readability. I think this is the more elegant approach with good encapsulation, although it's a bit more work to set up?