How do we design a control system with a mix of single-phase and three-phase electrical loads from a three-phase supply?
MCCB will distribute to a 3-phase transformer as well as few single phase equipment


That is not correct. The MCCB should connect to a distribution board that contains branch circuit breakers for various three-phase and single-phase loads loads. Alternatively, there could be two MCCBs, one for the transformer and one for a distribution panel for single-phase loads. There is also a question of why there is a transformer if the voltage at the MCCB is suitable for the small loads.

Two circuit breakers can be used as shown below provided that they are properly rated to protect the connected wiring and loads. The wiring from the circuit breaker in the factory distribution board must be sized to be protected by that circuit breaker and that circuit breaker must be rated to carry the current in the phase (marked C) that carries both connected loads.