Hi Peter,
So I found what is going on. The reason why it is showing an undefined reference is because the function itself for the SetupCapture is commented out as it has a macro definition preventing its use.
I noticed that there is a typo in the definition as it does not make sense to be not defined and the value be one as it is right now. Try this:
#if !defined(FSL_FEATURE_CTIMER_HAS_NO_INPUT_CAPTURE) && !(FSL_FEATURE_CTIMER_HAS_NO_INPUT_CAPTURE)
or as it is right now remove the exclamation mark at the beginning but define the macro at the beginning of the document.
#if defined(FSL_FEATURE_CTIMER_HAS_NO_INPUT_CAPTURE) && FSL_FEATURE_CTIMER_HAS_NO_INPUT_CAPTURE

Try this and let me know if it works out for you.
Best Regards,
Sabina