Typically serial links (including TAXI) always run at a single data rate frequency, which is derived from the REF clock. For example, if a 20MHz REF clock is used, the SPDSEL and RANGESEL can be configured to have a serial data rate of 50Mbaud, 100Mbaud, or 200Mbaud. When the link is idle (no real data is being sent), JK/LM idles will be sent by the transmitter according to the TAXI protocol to maintain the link. Thus the serial data rate will always be constant.
Using a spread spectrum clock to clock the link is not recommended because you are adding jitter to the signal, and it makes it more difficult for the receiver PLL to lock.
If you are planning on running at 100 Mbaud I we recommend using SPDSEL =LOW and RANGESEL = LOW, which will multiply the REF clock by 5 to get the serial data rate clock. We would also recommend using the CY7C9689A device in synchronous mode (without the FIFOs), since these synchronous designs tend to be easier to design and debug.