Yes, the possibility of different FTP would be nice. Until then I see the following workarounds:
Using Powermatch
Some powermeters have the ability to configure an adjustment factor which you could set so that powermeter matches the smart trainer
Manually setting different FTP per ride
Concerning the last point I created a more general feature request that could also be used to set different FTP for multiple rides in one step (so you could do it just once for all past rides based on a specific search criteria like power input). Maybe you want to take a look: