Hi
When Ethernet and USB are required together the 50MHz (or 25MHz) clock source can be used to generate 96MHz system clock. This is then suitable for the USB clock (by dividing it down to 48MHz).
100MHz can not be used as system clock, but the difference is fairly small.
To run at 100MHz system clock, an external 48MHz clock can be applied to the USB_CLKIN input when the chip used supportes this.
Regards
Mark