that is a good question, a not so elegant solution for now is to assume this is a normal process, and to create instead of the LCIA results the amounts of the respective reference flow per LCIA category (i.e., have 4kg CO2 emissions instead of 4 kg CO2 eq GWP) in this process.
You can also create "pseudo flows" (CO2 eq. etc.) and then add these to the methods, but this is even more workaroundish.
All the best,