We can implement collision detection between the back-to-top button and other elements on page. However, this is very taxing on the visitor’s browser and CPU, and open to weird results as well. For example, some plugins might add a transparent element that covers the whole page (e.g. a popup modal).
In the next theme update we’ll add automatic collision detection with the Recaptcha badge and move the button when collision is detected, since that is fairly commonly used. For all other elements, I’m afraid the most efficient solution would still be to manually move the back-to-top button via Custom CSS.