It's frustrating and time consuming to reposition the collision, everytime I change the scale a bit. Does anyone know how to change the pivot, so the collision stays at the center?

I'm trying to duplicate your problem, but when I use a similar scene, the three stay perfectly centered no matter how or what I scale. Even if I move one off center, it stays exactly where it's at relative to the others.

    Megalomaniak

    I added it in, but nothing changed. I can't get the things to separate. I must be missing something unless v3.5 fixed the issue.