This is sensible, AC coupling the inputs in your design will protect against common voltages that violate the TS3USB221 datasheet. These common mode voltages would be generated by the clock sources.

Our customer is using TUSB8041 to work with Novatek SoC and added 100nF AC coupling capacitors on USB_SSRX_UP pins for TUSB8041, but they found that sometimes it will cause USB3.0 communication ...