USB Type-C cables (and legacy cables) have only one CC wire. The wire indicates which Rx/Tx lanes to use. When connected, if CC1 is "active", it means "normal" plug, and the FUSB302 chip will inform the I2C host master over I2C interface about plug orientation (and port capability of the other side). Therefore the I2C host (your device) shall connect its USB3 data to Rx1/Tx1 lanes.
If CC2 is active, it will be the "flip" orientation, and your MCU should activate Rx2/Tx2 lane.
If you swap CC1 with CC2 on the FUSB302 inputs, the I2C registers will report inverse information. So you can do the swap, but you will need your MCU to invert a lot of information from the FUSB302 IC.