Use cases for the 2 functions are different.
String.prototype.substr() lets you take a substring from the end of the string using negative start value which makes it suitable for some more use cases without generating overly verbose, unreadable code.
// alert('1234567890'.substring('1234567890'.length - 4)) <-- UGLY
alert('1234567890'.substr(-4))
By that alone it makes the assumption in the question that the functions achieve the exact same thing simply wrong, and that makes it no different then asking why any other function exist. The only people who can answer such a question are the ones who made that decision.
