Thank you for your answer!
A spread-spectrum reference clock is permitted for the PCI Express and SYSCLK only.
According to Figure 4-3 on page 309 of the LS1046A Reference Manual, if a spread-spectrum clock is used for SYSCLK, it would mean that the USB PHY would be driven by a SSC clock. Is this okay?
Also, according to the same figure, the DDR PLL can have either SYSCLK or DDRCLK as its reference. Is it okay for the DDR PLL to have a SSC reference clock?