The only reason to do that is if you want files over 4 GB.
I have to say, if you're getting files that large you're wasting space by encoding at a bit rate that provides more detail than the iPhone can display anyway.
Let's put this in context:
Let's say you take Handbrake's default iPhone setting and you DOUBLE the bit-rate. So you're getting twice the data that Handbrake thinks you need.
Ok, then you encode a 3-hour movie with that. (Pretty long movie, but possible.)
Doing all that gives you a file that's roughly 2.5 GB. So I've got to ask, how are you hitting 4 GB files unless you're just raising the bit-rate beyond a reasonable number?