So keep in mind a couple of basics. The original instance of course has no transforms. Unlike Maya or other where a Group also has transforms. The instance itself has transforms. And it is a transform for the entire collection.
So what changes you make on the transforms of any objects at the object level will propagate to the instance.
The instance center will always be the origin center, 0,0,0, of the original scene from the original group. (by default - but check this great post which explains more options) The instance can then be placed anywhere and its local transform in the new scene will be the relative center of the old scene.
So keep this in mind when placing your original objects. Unless you always want them the same relative distance from the instance center no matter where you place the instance, keep them located at 0,0,0 in the source scene.
So this brings up two basic scenarios. You can have collections that establish a spacial boundary like walls and so on, or furniture in a room, or even an animation through space. And that entire space can then be placed anyplace in the target scene.
Or you can have objects, think of LW Layers that are always at 0,0,0 and then individually loaded into a scene and then transformed.
This in essence would be the way to replicate LightWave’s layer system in Modeler as it relates to Layout.
Your source scene becomes Modeler with your collections being layers and your target scene is layout with the difference that all transforms, animations, deformations could only occur in Modeler on individual objects. It is both limited and more powerful as your needs dictate.