Please find my comments to your questions:
>>May I know whether the frequency deviation of crystal will affect SS signal quality ?
Yes, frequency deviation will affect the SS signal quality.
>>If so, how does FX3 keep consistent signal quality for different frequency deviations of crystal ?
Please refer to section 5.1.2 of the application note AN70707. It contains information regarding the maximum frequency deviation of crystal that can be used along with FX3. The link to the Application note is given below:
>>For PCS_TX_DEEMPH bits of USB3.0 PHY Transmitter Config register, how much SS signal will change if it increases 1 ?
When the value passed to the API CyU3PUsbSetTxDeemphasis() is increases by 1, the deemphasis level drops by 0.187dB.
If following the crystal requirements as application note, the signal quality for different boards (same PCB layout) still has large difference. How to ensure the consistency of signal quality for that case ? Thanks.
Please check whether the crystal you are using meets the requirements specified in table 4 of AN70707. If the crystal that you are using meets all the requirements specified in the Application note, then please go through the schematic and layout checklists that is mentioned in page 28 and 29 of the application note.