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They accomplish the same thing with different dependency structures, as well as catering to different types of dependencies. Front-end components vs backend components.
FWIW the latest versions of NPM now flatten the dependency tree as much as possible, so the resulting structure is now much closer to Bower's. Also, I use NPM to manage all of my front-end dependencies, with great success, and it seems like most new OSS front-end JS projects these days do also.