This is a great question. If you use separate MOSFET and diode components, the current sharing (and therefore the losses) during reverse conduction of the overall device is determined by the path impedances of the MOSFET and body diode. If you have chosen not to provide on-resistance values for either device, the current will be shared equally between the diode and MOSFET.
You should consider the typical timing of the switching events. Can it be assumed that the diode conducts for only a small time during the interval before the FET is gated on? Are you expecting a specific current sharing behavior if the FET is reverse-biased? Or do you want PLECS to only consider the Rds(on) characteristic in this situation?
If you want the MOSFET to carry the entire current when it is gated on during third quadrant conduction, you can actually use the combined MOSFET and Diode component. I have attached a working example of this approach, which requires a little bit of explanation. The single thermal description uses Custom Tables that are called in the Conduction Loss tab's formula and are chosen based on whether the MOSFET gate signal is zero or nonzero. To easily view the example device thermal description, with this model open, go to the Window>Thermal Library Browser menu option and look for "MOSFET3rdQ_body_diode".
You should also look under the mask of the MOSFET converter and see that it looks as it normally does, but in fact, each device is reimplemented as it’s own masked subsystem. Looking further under the mask of one device you will see that a gate signal tag has been added, which is used in the conduction loss equations. You will see that at each subsystem level’s mask we are passing the gate signal by reference to the next higher level. Please let me know if you have questions, but I believe this implementation can be easily replicated and modified to include your own part’s loss data.