Interesting idea. I've made a sort-of working version at User:Yair rand/ReferenceTooltips.
A few points:
- In cases where the reference is very close to the reference section (both on the screen at the same time), duplicating the reference content in the tooltip probably isn't the best option. Maybe just give the reference the "targeted" color, or otherwise draw attention to it?
- This could get very annoying when users are just using their mouse to read through the text quickly, and the tooltips keep popping up...