Pin PC1 I have set as an output. As this is is also controlled by TCD I've ensured the FAULTCTRL register for that pin is disabled.
TCD0.FAULTCTRL = 0;
PORTC.DIRSET = 1 << 1;
I noticed there is only 2.1v at the pin and a scope showed that the pin has not been released from TMRD (I have a 2MHz 50% duty going). Microchip stated in a support ticket that is can be released for general IO usage?