Hybrid electric propulsion is a promising solution to reduce aircraft emissions, thus improving the sustainability of the air transport. In this work, a hybrid aircraft configuration with a rear-mounted boundary layer ingestion (BLI) engine has been investigated. The partial embedding of the engine into the fuselage generates a distortion of the ingested inflow causing additional tonal and broadband BLI noise sources, and, at the same time, alters the existing one, such as the rotor–stator interaction noise (RSI). This work is focused on the tonal RSI noise modeling, with and without the distortion generated by the BLI, and the far-field propagation including the acoustic masking contribution due to the engine–fuselage integration. As the main result, this work shows the contributions of BLI and the engine–aircraft integration on the RSI noise. Both effects should be properly taken into account in the early aircraft design stage for an effective noise reduction even at ground level.