Just tick the "Destroy on startup" attribute on any objects you don't want hanging around at startup. You will still be able to create other instances of them no problem.
It might seem ccluttered having things hanging around in the layout like that, but they have to exist somewhere. Perhaps in C2 there can be an "Object library" or something that you can store objects in and just pull them out as needed, instead of sticking everything in the layout (I am feature requesting this )
Cluttering the layout box means objects sitting there inside the white part, when they can just as easily sit outside it as there is NO distinction between white layout box and gray layout void beyond the use of kill outside layout commands (you can confirm that with the devs, I checked). Cluttering is the correct term used in development for anything within a player area that isn't required at that point in time (such as storage, as many games, even recent ones, use storage rather than load when needed), in the early days, space was at a premium so clutter was kept in small area's the player couldn't access (often seen in games such as Doom, unconnected black boxes containing a couple of enemies, would also result in enemy noises being heard at strange times). In layouts case they can be kept outside in the void as space is unlimited (without getting into the 32bit precision issue the further out you go from zero point, because it's too early and I'm still on my first coffee).