The shoulder yoke on the three-piece wasn't really that
much bigger than the (what I assume is an) all-in-one piece, an inch or two longer at most. Compare two random caps:
The badge looks far too far up even with the longer yoke. They could have put it in the normal place and it would have looked fine (IMO of course). Unless there was some physical reason why it couldn't go on the black part, maybe it kept falling off? I don't know.
The "Rapture" uniform/badge combo is also appears in most of "The Darkness and the Light" (where the left screen cap above comes from) until the last scene when they rescue Kira, where Brooks appears to be wearing the normal uniform with the V shape in the yolk and the comm badge in the correct place.