CGU_CLKOUTSEL.USBCLKSEL bits do not have any effect on USB operation. It does not effect the internal USB PLL clock in any way. It just divides the USBPLL clock by (N + 1) before routing it to CLKOUT pin(when USB_XCLK is selected in CLKOUTSEL field). These bits along with CLKOUTSEL bits can be used for debugging to see if USB PLL clock has locked to correct frequency.
USB PLL clock is derived from USB_CLKIN based on values programmed in USB_PLL_OSC register in USB module
