Welcome to the forum, Bobit!
Ad. 1) I don't think there is any special mechanics, but at 1 tile you are extremely unlikely to get a deviation big enough to hit your cover.
Ad. 2) It affects the gameplay by, well, the battlescape being in full 3D... So in all sorts of ways.
Ad. 3) Smoke weapons can cause extra effects on explosion, but the residual smoke will be normal. We can't have multiple smoke types.
Ad. 4) I was the one to suggest this feature. I realize it's not perfect, and some people don't like it because of this, but I will defend it to the death. It adds tactical depth and makes close combat look a bit less silly. True, the AI doesn't use it that well, but it is pretty simplistic in general, not just here. Also, "stepping back one tile" very often gives you a fistful of buckshot to the back. :)
Ad. 5) I'm not sure what you mean at all. Do you want a single level game, play-until-you-die style? If yes, I can help with it. But it's not related to a mod being a master (it's generally not important for 99% of modders whether a mod is a master).
Ad.6) Nothing widely known, but I remember some attempts. X-Com 1 is commonly regarded to be too easy to warrant this, and TFTD isn't that popular. But there is the debug mode for auto-killing enemies, seeing the whole map, etc.
Ad. 7) No, that would completely ruin the mechanics, which while simplistic is very tight and quite ingenious. Changing something this basic would probably require redesigning everything TU-related from scratch, and good luck beating Gollop here (though who knows).
Ad. 8) I am not aware of any mods making the game even shorter than vanilla. Maybe Survivors, but I haven't played it yet.
I hope it helps!