With APDU wrapping you can only wrap DESFire commands. The PPS command is part of the underlying ISO 14443-4 layer. In fact the PPS command is part of the initialization phase of the ISO 14443-4 transmission protocol. However, once you are at the point where you can transmit APDUs, the ISO 14443-4 transmission protocol (ISO-DEP / T=CL) has already been established. So at this point you cannot change any protocol parameters with the PPS command.
In general you can't change these parameters through javax.smartcardio
unless the smartcard reader implements some specific interface for re-activation of the card with a different data rate.