The Hexen blue armor (I think it's the one that replaces the FWeaponPieces), the Heretic Silver/Enchanted Shields, and the Chex armors will always leave green/blue (just blue in Hexen's case) armors regardless of the setting. Don't forget that the Heretic armors had different SavePercent values compared to Doom's armors. Strife leather/metal armor apparently isn't replaced at all, but they seem to function just like Doom's armors.
The Hexen blue armor (I think it's the one that replaces the FWeaponPieces), the Heretic Silver/Enchanted Shields, and the Chex armors will always leave green/blue (just blue in Hexen's case) armors regardless of the setting. Don't forget that the Heretic armors had different SavePercent values compared to Doom's armors. Strife leather/metal armor apparently isn't replaced at all, but they seem to function just like Doom's armors.