The Control Room Feature in Cubase Pro allows you to set up various speaker or headphone outputs for quick switching and listening comparisons. What makes this functionality even more useful is that each output scenario can have its own effects chain independent of each other.
Therefore, you could instantiate a Reference 4 plugin in each chain with the appropriate setting without affecting your bounced track. This is perhaps the easiest solution of all that has been discussed thus far. Cubase has essentially built-in the routing solution via its admittedly awesome Control Room feature.