Earlier quoted context omitted.
I supposed you are advocating two distinct Merkle trees? Because otherwise the prefixes will change anyway. But the only reason this would be attractive is because then people could keep using the existing prefixes to refer to the whole commit. But of course doing this would be insecure. So for this to make any sense at all, people would need to make good choices on when to use an insecure prefix and when to use the…
To be fair, the prefix problem would exist no matter what hash function would you pick. GitHub displays 7 characters of a hash, giving 28 bits. You could very quickly generate collisions with birthday attack in pretty much no time. Prefixes are always going to be insecure because they are so short. In fact, https://github.com/bradfitz/gitbrute exists.
Also: the prefixing increases the length of the hash (and hence the desire to shorten it) without adding any security.