Oh ya!If the plants are at the same stage they will be fine. If you tried to run one tray and then the other a month later for perpetual that might be a problem. The only other thing to watch out for is how often they are drinking the water. Just keep an eye on the reservoir level and ppm and you should be fine. You might have to top off more often but that's not a problem.
And instead of alternating, add a Y and flood both trays at the same time. You can still run one res and one pump.