Lack of imagination?

: I bet they are human shaped so they can be your ally at some point in the
: campaign and get in a car with you.

If that's true and if I pick up Halo 5, that would be the first time I've ever systematically exterminated my allies.

: Or maybe they're human shaped so they can extend a hologram around them
: self and pretend to be a human.

No.
Forerunner machines have force field generators and gravity manipulation technology and hologram projectors. They don't need limbs. And in Silentium, they had a device that let a monitor, a floating humming glowing lightbulb pass as a flesh-and-blood Forerunner.

They don't need limbs!