Function composition has one huge benefit over chaining APIs: it allows any combination of JavaScript functions to be stuck together to form a pipeline. One could create a pipeline involving a function from library A, a function from library B, a function from library C, and a built-in function. With a chaining API one is restricted to the set of functions available on the object facilitating the chaining.
I found this to be a problem when using Underscore. This would be fine for a pipeline comprised solely of Underscore functions (represented here by lower-case identifiers):
_(x)
.a(...)
.b(...)
.c(...)
.value()