By setting a culling mask on the player's camera, you can ensure it does not see the layers containing objects you want to hide.
By unchecking layer interactions in the physics collision matrix, you can ensure that the hidden objects won't process collisions with objects on other layers, so they'll just ghost through each other without sending
OnCollisionEnter messages and the like.
You can also use layer masks to exclude these layers from your raycasts or other physics queries.
Together, these features effectively put those objects in an unseen parallels universe, even if they are close by in coordinates.
You'll want to avoid moving objects too far away from the origin, due to limited floating point precision.
You can also put these objects in a separate scene file for ease of editing them in isolation, and use additive scene loading to load that scene and others at the same time. This does not automatically separate them for rendering and physics interactions, so you still need to use layers as described above.