EdDSA certificates are not really standardized or ready yet:
The reason that the error looks a bit funny is that the line of code that produces it has a mistake:
return berrors.MalformedError("unknown key type %s", reflect.TypeOf(key))
That %s should probably be %v.
e: opened a PR, but I noticed that the same problem seems to exists in vendored square/go-jose, not sure whether that problem is exposed in Boulder though.