Can you use the CCL "trivially" just to move a peripheral function to a pin where you couldn't otherwise direct it?
For example, on the ATmega4809, USART0 TXD can be moved to PA4 or PA0 via the PinMux, but it's also available as an input to the CCLs, which can output to PA3, PA6, PC3, PD3, PD6, PF3, or PF6. (and the pinmux can also disconnect it from the normal pins.)
(oh my: the CCL documentation has changed quite a bit since the version of the datasheet I've been looking at. It looks like USART1 and USART2 might be similarly redirected.)