First of all, I love the amount of work you put into your investigation. Its always nice to see motivated people looking to learn more about the nature of their problem and putting in effort 
The biggest clue as to what the issue is already in your experiments and initial problem statement:
I can even mix green and red bodies unless they’re not on the same side of yellow
I was wondering what if the green and red bodies don’t touch each other so i added a space between them. this is the only change compared to 2/a. (and there is extra space on the two sides but i think it’s not connected to this problem). merging was successful.
The problem with the original union, and subsequent smaller reproductions is that you are asking Shapr to create non manifold geometry by creating two solid regions which touch in a non-manifold edge:
If you were to merge these three bodies together the resulting solid would have an edge which has 4 neighbour faces, making in non-manifold. Such topology cannot exist in real life, thus Shapr refuses to do the merging for you.
My best guess is that the model used to work because you had the flat yellow surface on the screenshot slightly higher in the past, so that it would cover the problematic region like this:
You don’t need to raise the blue face so high: Making it so that it concides with the bottom flat faces of the green and red bodies would be sufficient too ahe planar red, green and blue faces touching would be deleted anyway as the three shapes are unioned together to represent a single volume. In this body the problematic edge would have only two neighbour faces once more.