(a) Water level at A.

(b) The air space between big stones are larger than airspace between small stones. With Setup Y, more water can fill up the larger space between stones, so water level in Setup Y will be lower than compared to water level in Setup X.

Note:
In theory, if the 2 setups were filled with different size stones up to the same level, the total volume of big stones would be exactly equal to the total volume of the small stones. For higher level students who have learn to calculate volume of spheres, you can verify this by calculating the total volume of different size spheres that can be packed into a given cuboid volume. The total volume of the spheres will be same, regardless of size of spheres.

So theoretically, the total volume of stones are equal, which means total volume of air space between stones are also equal, and the water level in the two setups should be exactly the same.

In practice, the situation is slightly different.
If you have ever tried pouring sugar, salt, milk powder, etc, into a container, you find that when the container is full, you can shake the container a bit and the contents will settle to a lower level. Then you can pour in a bit more material. The reason is that objects of smaller sizes can be packed closer together. This means with smaller objects, there is lesser airspace in between the objects.

Water Level C

Since Set-up Y has bigger stones, the stones will be heavier, denser and occupy more volume than the small stones. Hence the bigger stones take more place of the water in beaker Set-up Y. thus water level increases more in Set-up Y compared to Set-up X.