As for your original question:
Can prepopulating of fields possible from related list level even possible?
The answer is Yes. And it can be done the way you have mentioned by overriding the New button (and using a custom lightning component). The override is always applicable on the object you implement and not on the object it is related to.
So let's say if you override the new button on say object A, and that it is related to say object B, then when in object B's detail page, and in related list for object A, the new button on related list for object A will always be applicable on object A and not on object B.
Now how you can pre-populate the fields on any object? You can do so by utilizing the
defaultFieldValues parameter of force:createRecord. However remember as in its current form, you cannot pre-populate values from the parent record, i.e., in the above example, when you click on New on related list A, you cannot populate values from object B on any of the fields on object A. You can find more about this here on this idea.