I agree, modeling soffits that look appear correctly in ceiling plans, elevations, sections and 3d is very difficult, and usually requires some compromises. If you extend a ceiling for the entire base of the soffit you get a line in elevation and vice versa, and neither looks right in sections. The closest I've gotten to modeling it accurately is to add sweeps to the base of the soffit wall that miter in at the corners. It works ok, and looks right in sections and 3d, but still usually requires the division between walls and ceilings to be changed to invisible in the rcp. Joining sometimes works, but often doesn't. This method doesn't work well on corners that aren't right angles.
Then there is the issue of window heads and sills. While walls or families can be set to wrap at inserts it only applies to the jambs, requiring a lot of manual painting for the heads and sills to look ok in 3d