Converting to base64 generally increases the payload size. Being able to convert it that way is a workaround - not a solution to being able to transmit binary information.
I received two emails yesterday with application/octet-stream as part of the inner body, compliant with RFC2046 [0]. Having a Content-Transfer-Encoding of base64 is entirely optional.
It's the default for certain larger email hosts - that's the reason you see it frequently, but that in no way means that it is the _best_ option for a protocol that suggests it's solving the problems of the old one.