Since the introduction of weapon skins, it looks like the weapons skins from regular loadouts do not show up on the merc models during the pre-game team lineup (visible on all three merc below but most obvious on Turtle who's gun should be mostly orange):

Also, notice that the Javelin in the lineup is wearing a Nuclear Winter skin and carrying a Dreiss while her loadout card is Bronze with a SHAR-C. This happens every time you swap loadout for a merc in the game lobby (keep the same merc in the same slot, but assign it a different loadout card).