Erek's systems are vast compared to the tiny container, built to accommodate complex AI and a very long lifetime's worth of data. There's plenty of room to accommodate Jarvis while he ties up loose ends and plants some false readings to slow the Yeerks down. Most of his attention is focused outward, his functions tied up in managing sensors and holograms and planning courses of action. Most. And no matter how bizarre the sensation of someone else in his systems, there's also a sense of fierce satisfaction as he disconnects behind Jarvis. There's no way the Yeerks will catch them now.

Welcome aboard, Jarvis.