I just had another thought: this condition often presents itself when we have adjoining structural elements, whereas not so much for finishes where we typically hide adjoining material 'seams'. This is noted in Jared Banks entry within the referred topic. He speaks of framing and my experience is typically around adjoining concrete walls and columns, or primary and secondary steel, etc.
Perhaps you could have a Work Environment (or project template level) panel where you review the coplanar separation value defaults by classification (e.g., 'structural') or perhaps MVO, so as to set most of your element groups from the start. Then, you customize at the element level check box as an override to those more global values.
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