The cut out is to relieve pressure in the perineum area so you can hopefully avoid ED, numb nuts, and other issues. It is not for ventilation. The cut out can be a channel or all the way through. It makes a big difference for a lot of people.

Women benefit from the same type of relief channels although the shape may be different and the construction of the saddle may be different as well.

The padding in bike shorts will not affect the saddle cut out, but you will often find in nicer shorts that the padding mimics the saddle shape. They are designed to work together.

“Ventilation” in the shorts comes from the wicking nature of the materials used.

For longer distances, wear bike shorts with a pad. They should fit somewhat tight to take advantage of the compression and avoid chaffing. You will find a benefit. Don’t worry about the diaper look. On short rides around town, wear regular shorts.

You don’t want your bike shorts moving across your skin. That’s how chaffing occurs. Don’t worry about whether the bike shorts slide across the saddle. It’s all commando under the bike shorts. Everyone does it.