I heartily encourage this endeavor. Some thoughts:
Balancing the two players - You're developing more and more ways for the dwarves to win, and this is good. Having "the 'evil' player runs out of cards" be a victory condition is terribly unsatisfying, not to mention impractical if deck composition ever changes (i.e., you make a single expansion). Think of some other game with clearly different sides, like Netrunner: the "evil" player in there owned the victory conditions. That is, the Corporation player put Agenda cards into play, and both players wanted to score those cards in order to win. What if your "hazards of the world" player somehow controlled dwarven victory conditions? Either, say, by dispensing the goodies themselves ("upright masterwork adamantine sword"), or by having attempts to kill the dwarves grant "victory points" if the dwarves survive them?
Keeping the feel of DF - I hope "making a fortress" is central to dwarf play. The "layers" idea struck a chord with me: yes, it would require re-thinking the game, but it fundamentally enforces gameplay around "digging a fortress in the earth." But I also see that layers could be annoying if players have to memorize the pattern (instead of having a computer game track it). You've spoken about your card layout plan: could you go into further detail on how the player "makes a fortress" in your scheme?
--Rexfelum