My flood tray was about 6 inches deep, but I didn't flood it to the brim, the top layer of hydroton never got wet. The pots were about 7 inches tall, but usually, the plant was an inch or so settled down in. I didn't want to have much root ball trying to grow or survive outside the typical flood zone of the tray.
You can use the 5 inch pots, I would not veg longer though or the plants will get cramped. Just use more of them and if they average 5 grams lighter each it won't matter because you will have more of them.