Clay floor is designed to be hard, not draining because the bedding soaks up the urine.
With clay under the mats, the urine is not soaking into the bedding, not draining away
either so you get a mess.
I love rubber mats, use them in every stall. However our stalls were designed for drainage,
with various layers to take any wetness away that goes thru the rubber mats. The rubber
mats are soft to lay on, very easy to clean each day. I wouldn't have a naked dirt floor, too
hard to clean and keep leveled. Poop sticks to it in cold weather, so it is hard to clean well.
Clay is an old time stall floor, because it was not as slippery as wood, harder surface to keep floor
level and easier to clean that bedding out. Determined horses could still dig holes or get
the floor uneven, so you just planned to refill the stall floor as needed with more clay.
If you should decide you MUST use rubber mats as flooring, you will need to dig up that clay
and refill the floor with draining materials like crushed limestone and gravel mixes, stone
dust as the top layer. You will have a better floor if you dig down almost 2ft, to start
those thick drainage layers.
Rubber mats ARE very useful in other places, just not good on clay stall floors. I have
them in front of the barn doors so it is not muddy when driving the tractor inside. Under
gates where I catch horses to bring them in, so my boots don't get sucked off!