Graphene flakes acting as photonic nanoantennas may sustain strong electromagnetic field localization and enhancement. To exploit the field enhancement, quantum emitters such as atoms or molecules should be positioned in such close proximity to the flake that electron tunneling might influence the optical and electronic properties of the system. However, tunneling is usually not considered if the optical coupling mechanism between quantum emitters and nanoantennas is at focus. This work presents a framework for describing the electron dynamics in hybrid systems consisting of graphene nanoflakes coupled both electronically and optically to adatoms and subject to external illumination. Our framework combines the single-particle tight-binding approach with a nonlinear master equation formalism that captures both optical and electronic interactions. We apply the framework to demonstrate the impact of electron tunneling between the adatom and the flake on emblematic quantum optical phenomena: degradation of coherent Rabi oscillations and quenching of Purcell spontaneous emission enhancement in two-level adatoms in proximity of triangular graphene nanoflakes.