This is a phrase that has been in use since before America was a thing. It may not be formally correct but is just a shortened form of expressions such as "how is it that this has come about?" and has been shortened to versions of "how come" since before Shakespeare. There was thus already significant overlap in how one might have responded to questions of "how come" (original meaning) and "why".Of course there is the common question (probably when English isn't their native language) of "how come" instead of "why".
As for being used synonymously with "why?", this is a mid-1800s development. In England. By people who spoke English. English people this side of the pond use it all the time.