Hi there, obviously the auto will get less light, so it will grow a bit less and will have impact on yield in comparison with 18/6, however if your growing environment requires this, then so be it.. i personally would not go through the hassle to move plants around constantly. Especially if you can't be 100% sure that there will not be any light-leaks, as this would be very bad for the photoperiodic plant.
I know people with a single tent or box and they grow mixed setups in the same area and still get good results.