How does spread spectrum clocking on the USB interface affect my communications channels such as the UART?
The USB interface uses clock recovery to sync to the input data stream from the host. We have not characterized the affects of spread spectrum clocking on the USB signaling from the host; however, the clock recovery feature within the MCU should be able to recover the data.
As for the UART, the USB clock recovery is making changes to the USB oscillator frequency. When the internal oscillator updates its frequency, it affects the SYSCLK (if the USB oscillator is selected as the SYSCLK source) which drives the MCU. That change will translate to the UART as well if it is also driven from the same clock.