My guess would be that multiple layouts are not the tool you might be looking for in that case, but rather have one layout for, lets say the entire Brinstar region, lock the camera inside the current room, and when you go through the door, Samus stops inside the door, the camera moves from the current room to the other and locks inside it, then Samus goes to the other side of the door, however if the enemies continues to move, you might have the risk of them going inside the door and hurt you (which happens actually in the first Metroid sometimes, not complaining but that was buulllllll*hit).
Doing this however requires to manage enemies and items carefully so the game does not have too many things to compute (being inspired by the original Metroid on those choices can be a fine idea.), and I will admit this is not something C2 helps a lot with (Being able to scroll from one "layout" to another would be easier, but it is not possible).
My one of my attempts was to use zone-based camera movement but it was impossible to make an area that had both horizontal AND vertical movements (i.e. one shaft is just horizontal, another is vertical) in the same room because it would break immersion, could be glitched by walking back and forth (so the camera is constantly switching zones) and such. So if I did revert to that, I would have to very carefully design the rooms not to include such things.
As for stopping in the doors, I just made it so that when the player is overlapping the door, it disables controls and simulates the player going in the current direction and the door closes behind him. E.g. if he's facing left when he walks in the door he goes left.
I remember that, it was really annoying to get into a room with Flyers (the ones that fly out of pipes) only to get killed when the room is transitioning.....
An event like "Play is overlapping Sprite Room X | Destroying Enemies not overlapping Sprite Room X" would control deleting enemies the player is not in. While something like "Play is overlapping Sprite Room X | Restore Enemy (Family) Overlapping Sprite Room X".
But I doubt the actual would look exactly like that.
Trivia: You know the new System actions "Reload Layout X1, X2, Y1, Y2" and "Restore Persistent Objects"? I started the thread and was among the people who got ashley to make it. They were actually put into Construct 2 for this exact reason.
Thankfully, Construct 3 will have an Editor SDK, so multi-layout connections could be possible.