A practical quantum computer requires quantum bit (qubit) operations with low error rates in extensible architectures. We study a packaging method that makes it possible to address hundreds of superconducting qubits by means of three-dimensional wires: The large-scale quantum socket. A qubit chip is housed in a superconducting box, where both box and chip dimensions lead to unwanted modes that can interfere with qubit operations. We theoretically analyze these interference effects in the context of qubit coherent leakage. We propose two methods to mitigate the resulting errors by detuning the resonance frequency of the modes from the qubit frequency. We perform detailed electromagnetic field simulations indicating that the resonance frequency of the modes increases with the number of installed three-dimensional wires and can be engineered to be significantly higher than the highest qubit frequency. Finally, we show preliminary experimental results towards the implementation of a large-scale quantum socket.