This solution will work in any case. In other words, the engines that are necessary for the required movement will always be activated.
However, if, for example, you have asymmetric pairs of engines with different thrust and any angles, and you act on Rigidbody through engines as now, then there will be side effects. For example, you have right-hand engines: the first with 1 kN and the second with 2 kN that are located at the same distance from the center of mass, and if you use my dot product approach to get acceleration to the left, then both engines will be activated at maximum power, and in addition to the linear force of 3 kN, you will also get torsion. To avoid such side effects, dot-product alone will not be enough and in order to accurately determine what the thrust should be for each engine to provide the necessary torque and linear acceleration, you will have to solve the linear programming problem. Alternatively, use a direct impact on Rigidbody, and use thrusters only as a special effects emitter, and in this case, you will only activate special effects using dot-product. which will be logically similar to realistic ones.