Halflings can survive because nobody cares very much about them and they aren't very much involved in the world. They don't stand out or go on great campaigns of war like the tall ones. That's the specialty of both these halflings and their inspiration.
Anyway... I think we discussed the issue of what "from scratch" means earlier. Although having different opinions of it is fine... well, it is a fantasy setting as is. Or at least mostly one. Didn't we sort of agree earlier that therefore you would very likely want to have such as gold, silver and steel? Diamonds too? "Draw iridium, villain" not sounding cool and all that. I think the same applies and we will eventually want to have the staples... or get them anyway, alternatively, done with less consideration, difference and imagination, when someone decides to "just do it" (allowing which is a staple of this project).
Hell, the original idea was to make something which
resembles Dwarf Fortress but is made entirely by the players and works differently. Not e.g. a Starcraft-inspired space-themed total conversion which could have been the outcome if we had had enough fanatic Starcraft and sci-fi fans at the start. Not saying that that couldn't still be an acceptable outcome but... my original idea was to make a different fantasy setting to play in, with different mechanics.
Now, there exist fantasy settings where all is alien and nothing is recognizable. But those seem to me to always be much less popular for a story and for players. And I do sometimes get the feeling that while different is cool, the tagline shouldn't be "DF from scratch - weird for the sake of weird".
I should think that creating things with the
same name but different role in the story is fine. Such as you would make wolves or bears. Remaking the same stuff as is in vanilla is pointless, exactly as you said. Here I feel that those concepts of humans as a minority, mostly insignificant and either dark and dangerous or sad are sufficiently different to propose; they
force the player to relate differently to humans; the latter concept even has your species auto-killing them as scum in fort mode. Their body mechanics wouldn't be the same made from these templates either. Definitely not vanilla. I also think that being able to play as a "human outsider" which a human civilization brings can make for amusing stories with that perspective.
So that's my point of view, but I want to distance myself from saying that as any sort of administrator here. Rather as one of the modders as my opinion of what kind of content we can make.
But the last word is of course that if the people who enjoy this setting largely feel that humans would detract from the setting then they probably shouldn't be made.