Is it that annoying? You just need one unused layout in the project where you dump a single instance of every object in your game, then you never need to worry about this.
It's kind of a quirk of the engine because if you create an object and there are no instances anywhere in the project, C2 doesn't know what to use for the object properties. It's one of the things on the todo list for a long time but I thought it was minor and it's a little tricky to fix.