How to properly rig your character?

I’m new to rig & animate, so I check the work of the expert here. But I don’t understand why the rig control is blended with the skeleton


When it blends like this, how can we export the clean character (clean exported character: only contains the skeleton & meshes), I mean in this case, the export file may contain the rig controls & other data that won’t be needed in game. Does anyone know what’s the idea behind this?