A method for making a three-dimensional (3D) part with an electrostatographic based additive manufacturing system includes establishing first and second control parameter profiles, establishing a transfusion sequence, and transfusing n+m layers on a bonding region of previously accumulated layers of the 3D part according to the transfusion sequence. The first and second control parameter profiles each include a different combination of temperature and pressure parameters usable to transfuse a single layer of the 3D part. The transfusion sequence specifies the use of each of the first and second control parameter profiles in a specified order. A total thickness of the n+m layers is less than a thermal diffusion depth. The transfusion step includes transfusing n layers according to the first control parameter profile, and, after transfusing then layers, transfusing m layers according to the second control parameter profile.