merge or intersect mesh?

Which case is the best for perfomance? (both cases have a same material)
Please say your opinion.

case 1

case 2

For performance the second case is better.

As long as you don’t want the object to be transparent there’s no reason to split the top face of that trapezoid. If you create those meshes in a modelling application you might want to remove the bottom circular face of the cylinder. It doesn’t matter if the objects intersect as long as the two objects don’t have a face at the same depth value. This would cause z-fighting.