Best practice for hiding gameobjects in scene and game mode

I converted a large CAD assembly of a machine to gameobjects. Many of these gameobjects, like the machine's enclosure, block the visibility of other gameobjects inside the machine.

I want to be able to change the visibility of these gameobjects and I want to learn what would be the best practice.

At the moment I created layers to group the gameobjects that I want to show/hide by showing/hiding the layer. This works for scene mode and also for game mode when I set the required culling mask on the camera. Would this be the best practice or would there a better way to do this?

The problem starts when I enable object selection in the realvirtual controller. All gameobjects will be visible in game mode when this option is enabled, without taking the culling mask into account. What should I do to only show the gameobject that I want in game mode?