Therefor, why not make a couple of kit skins? For Bomb and Grenade Kits it could be just some good looking backpack, Toolkit could have some fancier looking wrench, Elixir Gun would obviously re-skin the gun as well and the same goes for Flamethrower. It also doesn't need to be a lot of skins, just something distinct, say 2-3 skins per kit, some could possibly work for multiple kits (such as Bomb and Grenade).
As for how to apply them, I don't think it would be so much of a problem to create an additional Equipment slot, POSSIBLY even make it a skin for the Back item (or an actual stand-alone back item) for engineers only.
I've always wanted to be able to equip a Flamethrower like this: