It depends on how the application is implementing the interrupts. MQX can build a interrupt table so that the MQX master inerrupt routine can determine if a valid user interrupt was registered and then jump to it. Interrupts can be setup such that they are added directly to the vector table so if the vector table is in RAM is would be different from the ROM version. But in general it should be mostly the same.
Read up on the various interrupt registering methods in the MQXUG.pdf in the MQX/doc/mqx path/ called "Handling Interrupts and Exceptions".
