Instead of using the Morph, I use a wall and a door or window for the opening. I use the Cadimage Tools Doors & Windows for the arched openings, but there should be something in the standard Archicad library that could do the same thing. The screenshot shows 2 different walls and openings because the client wanted a reveal around the openings.
In this instance, the corner has a column and the walls intersect with the column. Since the column material is the same as the wall material, there should be no line.
As far as your original question, I have encountered the same thing. I either have to deal with the line, or make the Morph element aspect larger, so there is no line.
Hope this helps.
Jeff