It is NOT the operating system that controls the time until an interrupt is handled. Why do you not have a look at the datasheet of the ARM Cortex-A7 Quad?
When an interrupt comes in, the microprocessor will finish the current instruction, save the return address on the stack and start immediately to handle the interrupt routine.
This usually requires only 3 to 5 clock cycles.
And if one chip runs at 16MHz and the other one at 900MHz - which one do you think will start and finish the interruprt routine faster?