In my testing it is best to just avoid having subspaces overlap or exist one inside the other as NPCs don't always acknowledge the distinction and still cannot cross the borders. Are you talking about an interior that behaves like an exterior, or an exterior worldspace here? If it's a worldspace, what you want to do cannot be done without making those sections interiors. If it's an interior, you're almost always best off using more that one interior so that the scene is less complex and so that things like pathing, detection, crime handling, and ownership work properly. If you MUST have all of it in the same interior, having the primary area being normal space, and then encapsulating smaller spaces within their own separate subspace is the best way to go.
If you're having problems with NPC movement, you can usually solve it by either changing some of your "aesthetics only" NPCs to use packaging that doesn't have them moving to any other space, and ensuring that every NPC who uses a load door has low level processing enabled. Even a few dozen low processing enabled NPCs running in the background doesn't require as much processing as a single NPC in the loaded area who is moving around within one of those partitioned spaces.