There are lots of imbalances but this confused me.
Weird Material Imbalance
That's a question about Stockfish, not chess. Stockfish evaluation can be very far out in unusual situations. Check out its evaluation of a few of the draws here
https://www.chess.com/forum/view/fun-with-chess/5-1-draw-contest
They should all be 0.
Having said that, its evaluation is no doubt because the rooks are more difficult to bring into play than the queens in the position you give. If you were to remove the pawns the evaluation would probably be very different.
Stockfish gives a -4 Evaluation
Given the circumstances, does a -4 really mean that much, and why is Black better here? I used the two rooks to queen ratio and black is still apparently better