Well, it wasn't meant to be proposals, more like questions for guidance in case I've missed something

3) Right click on the item and click "Master Lock" to lock/unlock a crate
Yes, but it seems like the required lockpick level is just hard coded in the furniture, so, for example, I couldn't find the way to place a sturdy chest with a very simple lock.
10) generally i dont see a way of preparing a new scene with placeables (players must be same scene as i could get it so far)
You could do this in Prepare mode, during your scene planning.