High-fidelity modeling of control surfaces is crucial in designing new aircraft equipped with active control systems. Since sealing spanwise gaps between lifting and control surfaces poses a significant geometric challenge, these gaps must be thoroughly considered in aerodynamic analyses of novel configurations. To better understand the effects of such gaps, we examine here the transonic flow through the spanwise gaps of the Benchmark Active Control Technology model, with trailing edge control surface deflections of \(-9.9^\circ \) and \(-5.0^\circ \) . Using RANS and wall-modeled LES turbulence approaches, this study reveals large, counter-rotating streamwise vortices and substantial streamwise recirculation zones, both highly sensitive to the control surface deflection angle. Results also indicate that RANS models are an efficient alternative for small control surface deflection angles, while wall-modeled LES approaches would only be advantageous at larger deflections.