PIE encoding and SPI communication
There will be no issues.
Infact, PIE data will be the payload for S2LP.
S2LP will use its own bit and frame synchronization method.
S2LP won't use PIE synchronization method.

Clock synchronization is internally handled by S2LP.
Your microcontroller will receive an IRQ interrupt request from SL2P whenever a packet is ready.

You may program your S2LP to output its synchronization clock but that's useful only if you want your microcontroller to do data recovery and data synchronization.
I would leave your S2LP both clock and data recovery unless you want to test your own protocol.