Future quantum networks are expected to integrate a heterogeneous combination of quantum systems, owing to the diverse advantages offered by different physical platforms in terms of scalability, coherence times, and interfacing capabilities. Within the context of this emerging quantum communication paradigm, this paper presents an analytical comparison of two photonic encoding schemes—time-bin and Fock state (single rail)—in hybrid quantum systems where flying qubits are entangled with stationary matter qubits. We evaluate their resilience against fiber channel and quantum transduction effects by calculating the fidelity of the final states relative to their ideal forms. Employing the characteristic function approach, we derive analytical fidelity expressions and investigate their dependence on parameters such as transmissivity, noise levels, fiber length, and source generation success probability. Additionally, we simulate the scenario with a dedicated QuTiP software implementation to verify the validity of the theoretical models. Our findings reveal that due to its inherent single-mode structure, the Fock state encoding consistently outperforms time-bin encoding in fidelity, as this structure significantly minimizes susceptibility to losses compared to the two-mode nature of the time-bin scheme. This analysis offers valuable insights for future hybrid quantum communication and information processing applications.