Fiat, my Zygo is planted just above the media, the roots when actively growing, at times, they naturally go into the source of moisture. Being sympodial in growth, it naturally makes pseudobulbs horizontally then may climb up like seeking more light as it goes. I just keep the old pseudobulbs there it helps provide energy for the new growth. As I have mentioned earlier it goes into a rest period, which in my growing area often happens after Spring to whole of Summer, when our temps are just so hot and dry, but I still give it watering. Then when temps start to cool down in Fall, it triggers that psuedobulb formation, and more active roots. The new flower spike comes from the new pseudobulb, so if things go well, I may have a flower spike in Spring. My zygo had a bad handling this year, unfortunately, since I was away in late June for over a month just when our temps were hitting several triple digits high and it had a long period of no watering, thankfully it is at its rest stage, just glad to see now it is active again.
Now going back to your zygo, if it were mine I will not repot yet, wait another year and observe first how your plant grows. Just be mindful of your watering intervals, it is already going in the cool season, as much as they like water, you have to give them proper intervals, to avoid rotting the roots. Do your watering early in the day, so by night time water has drained out.
As with most orchids, over potting is not recommended, you will not want those roots to stay way too moist below media level, it might rot, especially when temps are cooler and takes much longer to dry out, especially if it is growing indoors.
