Yes, Stratix® and Arria® family GX/GT/GZ transceivers can handle Spread Spectrum Clocking (SSC).
You need to make sure that Spread Spectrum Clock device adheres to the modulation frequency (30-33 KHz) and frequency spread (-0.5%) requirements for PCIe and SATA/SAS applications.
SATA applications require the rate matching logic to handle a PPM difference from 350 to -5350 PPM, due to SSC downspread. Rate Matcing FIFOs embedded in GX/GT/GZ transceivers cannot handle this high PPM difference. You'll need to implement the rate matching logic in user logic to compensate for this high PPM difference.
PCIe specifications require the SSC source to be the same on both systems. Due to common SSC source, there is no PPM difference associated with the spreading at the receiver. Hence, rate matching FIFOs embedded within GX/GT/GZ transceivers can handle the nominal PPM difference of /-300 PPM.