I'm sure there are exceptions to the rule, but most truck headers are made for the "low port" exhaust used from 66 and up. From what I see, most header applications listed say they fit 65-76 F-100s so I guess they assume the majority of trucks will have the low exhaust port.
You're correct that both sets of heads are car applications, but they did change the exhaust port height to help fitment in shock tower cars.
The C6AE has a lip at the top of the exhaust port that matches this lower port height, whereas the C4AE is a taller port that will be tough to seal with headers made for the low port.