Sorry, my computer crashed, took a bit longer to restart.
Here is my answer
In your scenario, your locomotive including parts (they are sprued) is 1 part and thus 1 footprint.
The train, 2 spheres and 1 pyramid are connected by the sprue, so it's 1 part.
I think, regarding the first part of your message, there is some confusing as to what we mean by separating.
If those 2 spheres and 1 pyramid would not have been connected by that sprue, they are seen as individual parts.
This means the tech is able to just move those 2 spheres and 1 pyramid and place them next to the train on the floor (so all the red support material you see below them aren't needed.
TL/DR:
If sprued, we cannot dissemble them <-- part footprint is calculated as one (see the green area in my picture)
If not sprued: techs will move them wherever they see fit. <-- part footprints are calculated individually
Please do let me know if it makes sense