As explained above, a shifted reference plane negates the effects of one or more transmission lines using circuit theory after the simulation of the entire circuit. This concept is shown in the picture below:
Notice that reference planes do not remove the transmission line metal, but only negate it. Shifting a reference plane is not the same as removing the metal from the simulation:
A shifted reference plane does not remove the fringing fields due to the step in width. This concept is illustrated below. Note that the fringing fields still exist in the final Sonnet results after de-embedding.