The CTC input needs to be 8b10b decoded data (a K-control bit, and an 8-bit hexadecimal character). If 8b10b decoder is bypass, the data at the input to the CTC block will be 10-bit encoded 8b10b data. So, it cannot use the CTC functionality when the 8b10b encoder/decoder logic is bypassed.
The other option is to disable both the CTC and 8b10b functions, and build the 8b10b encoder/decoder and CTC logic in the FPGA fabric.