You can still get into commander mode!
Somethign i found out today when I switched to the new FGD, when you put down the point entity for the command station in your map and then you are in the map in NSTR, while you don't see a command station, you can still press Use on the point entity (or at least where it should be) and it'll still throw you into command mode. just stand near where its supposed to be and slowly walk while stabbing your use key over and over again :)
this way you don't have to worry about switchign back and forth between two FGD's just to get into commy mode...
Russell 'DOOManiac' Weed