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.
It was enough of an issue for the costume department not to place it with the black part of the uniform like everyone else's. But the first screencap you provided is actually from a later episode when it really is just a case of the combadge placed higher than it needed to be (more on that below).
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.
"The Darkness and the Light" was when Brooks got his better-fitting costume, but his combadge was still initially placed in the yoke area as it was in the previously until it was corrected during that same episode. Your initial screencap came from the early part of that story before it was fixed.
His original one in "Rapture" was bulkier (to accomodate the vest underneath) and also lacked the branch-colored piping around the cuffs.