We employ a recently developed quantization scheme for quasinormal modes (QNMs) to study a nonperturbative open cavity-QED system consisting of a hybrid metal-dielectric resonator coupled to a quantum emitter. This hybrid cavity system allows one to explore the complex coupling between a low $Q$ (quality factor) resonance and a high $Q$ resonance, manifesting in a striking Fano resonance, an effect that is not captured by traditional quantization schemes using normal modes or a Jaynes-Cummings (JC) type model. The QNM quantization approach rigorously includes dissipative coupling between the QNMs, and is supplemented with generalized input-output relations for the output electric field operator for multiple modes in the system, and correlation functions outside the system. The role of the dissipation-induced mode coupling is explored in the strong coupling regime between the photons and emitter beyond the first rung of the JC dressed-state ladder. Important differences in the quantum master equation and input-output relations between the QNM quantum model and phenomenological dissipative JC models are found. In a second step, numerical results for the Fock distributions and system as well as output correlation functions obtained from the quantized QNM model for the hybrid structure are compared with results from a phenomenological approach. We demonstrate explicitly how the quantized QNM model manifests in multiphoton quantum correlations beyond what is predicted by the usual JC models.