why does the flow need to decelerate (by a thermal throat) in a scramjet?
I found an answer, for those who are curious. The thermal throat described in a scramjet is not an ideal case. Essentially, when the flow is supersonic, heat addition done in the combustion chamber can slow the flow down to subsonic speeds (based off the 1-d heat velocity, Rayleigh Flow). When this happens the flow is considered thermally choked, and is a bad case for this engine. To prevent this thermal choke from happening, the area of the combustion chamber increases with the direction of the flow (area increase increases velocity for supersonic flow).