Some outfits look better than others with armor pieces. True some pieces do clip pretty bad, depending on what you combine. I mean Army Fatigues, combat armor doesn't even FIT on them snug like they do on a Vault Suit, even though they're Army Fatigues!!! You'd think they would of made Army Fatigues, Dirty Fatigues and Military Fatigues tailor made to work with Combat Armor, but nope. Tragically Bethesda cut most of the clothing out of the catagory as under armor as they didn't want to do a Saint Row 2 style 'remodel' everything counting on what you're wearing. Tragically the clipping issues are horrific with that mod.
With that mod you don't have to struggle with under armor.