You can understand it like this:
This is an example of separating an object, I'm going to draw a luxury table from the French court, consisting of a large table board and 6 table legs, the large table board is 1MB, each table leg is 1MB. if you export the OBJ directly, then naturally it's 7MB. or you split it up and lay it out in a SH3D file 1 large table board plus 6 table legs. You save the file and see it's 2MB because those 6 table legs are the same and add up to a 1MB.
The same big tree why take up a lot of file space, because he has thousands of leaves, each leaf is very large, let's break it down, a trunk plus thousands of the same leaves. 0.5MB (this is a bit exaggerated)

I understand and recognize the principals like you described. Im a professional developer and the idea is similar to object oriented programming.
But that is not something that can be done by using OBJ/MTL files. The OBJ file format has no mechanism to define a part ("object") and then use references with coordinates to display that part ("instances").
That leaves converting to another format. For example converting OBJ to gLTF gives a huge reduction in size. I think the conversion does something similar to what you described. I'm going to try that for display of one my large projects on a web page. The disadvantage over the Sweet Home 3D html5 export is that you loose the options for level choices and 'walking' through the project. But at least it should load and move.