I am not an expert of PPjoy, but I know how SmartPropoPlus (SPP) works.
SPP, when placed in the FMS directory, emulates the computer's joystick functionality. In other words, FMS 'thinks' that it is communicating with a joystick (Standard or PPJoy) but in effect it communicates with your Tx that is connected to the audio card.
There is no sense in allowing the control of FMS from 2 Tx simultaneously, so I don't see any problem with this feature.
If you want to move from SPP to PPJoy, you just have to remove file winmm.dll from the FMS directory (or just rename it).