It appears that both naming conventions originate with Galen, the Greek physician, almost 2000 years ago (for example, see: Singer, 1952).
Although the precise motivations behind the naming conventions aren't entirely clear, it seems that the origin of the coracoid naming convention is quite simple: Galen thought it looked specifically like a raven's beak, as you state, rather than the beak of some other bird.
Fortuine (2000) seems to suggest that the origins for both words originally applied to beaks of different birds, which implies that Galen may have thought some bone structures looked like beaks of one bird, and other bone structures looked like the beaks of another bird, so he used the corresponding terms of description. Specifically, "korōnē" may have referred to a crow or cormorant (I feel like the cormorant link makes more sense, though both are supported by Arnott (2007) - it may not be possible to know how the distinction was applied from surviving texts), as well as referring to a hooked shape. The same source mentions several other bird-derived terms, including the coccyx resembling the beak of a cuckoo and "rostrum" used more generally for beak-like structures.
Today, coronoid and coracoid may sound similar enough to be easily confused by students of medicine. However, giving these different bones distinct names does allow for some useful shorthand, such that one need not refer to the "coronoid of the scapula": I would assume, though I'm not sure if it is possible to find a good reference on this, that this is the motivation to keep things as-is, besides of course the history.
Arnott, W. G. (2007). Birds in the Ancient World from A to Z. Routledge, New York.
Duckworth, W. L. H., & Lyons, M. C. (2010). Galen on anatomical procedures: the later books. Cambridge University Press.
Fortuine, R. (2000). The words of medicine: sources, meanings, and delights. Charles C Thomas Publisher.
Singer, C. (1952). Galen's elementary course on bones.