Scene Organization in blender2.8

Having some problem with scene organization.

I have a master scene that keeps all the models and also some different scenes with unique objects setup (objects in different location, different camera angle…). And here is the goal I want to achieve: I want to use those unique scenes to render my final works, but at the same keeps those object linked. Thus, whenever I makes some adjustment at my models, I don’t have to dig into every scenes I want to render to do adjustment.

I use Make Links >>> Objects to Scene to link my objects. However, things didn’t go well. Every time I move, scale and rotate an object in one scene, it will somehow change location, rotation and size in other scene. It seems like blender links the whole object across my scenes. But what I really want to link is the object data.

Currently, My solution is manually create new objects in different scenes and assign those object data to my new created objects. Fortunately, this method works well, yet it is way too tedious that it almost drives me nut. Is there a better way to speed up the entire process or do you guys have any scene organization tips to share with me. I will be very appreciated.

Long story short
This is my master scene.

This is my first setup scene.

This is my second setup scene.

I link Cube_01, Cube_02 and Suzanne across different scenes but I can’t position them without affecting other scenes

This is the example file.
Scene_Organization.blend (229.8 KB)