All feet in the door are not the same. When you're iterating on ad concepts, maybe CPC is an okay metric, or at least an early indicator. But these ads weren't really interations. Without a baseline CPA and running ads related to the ad that generated that baseline, CPC has no context.

Also, if all traffic is going through that to-be-optimized funnel, how does that justify ignoring the CPA of any individual lead source?

The only explanation that makes sense is that conversions aren't frequent enough to find significance. That makes more sense given how many variations were run. In that case, it doesn't make sense to run so many variations. That, or maybe find an in between metric that at least indicates some greater level of lead quality.