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?
Yes, I know it is unsatysfying but it may happen eventually and I have to find a solution for that state. Although main goal for dwarves will be acquring wealth factor (or something called similarly). Eg. you may produce some artifacts, deploy some nobles or build some buildings that are not resource efficient (costing much more than providing) but they give those wealth points that count towards winning the game.
Your idea seems interesting although I have one concern with it. There is a problem, how to make the evil player provide constant challege for fortress, so the both players can equally play and enjoy the game. This would greatly discourage 'evil' player from taking actions that may fail. I fear the game could become somewhat passive.
But you actually gave me some insipiration. There can be another victory condition. Dwarven player may call 'final resolve' (or there will be such card) that lets the 'evil' player for more actions for limited time, after surviving that dwarves win.
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?
It is essential, but I can't make exact tabletop copy of DF. Eg. I can't make herbalist specific card, because his role in DF is rather limited most of the times. Therefore I merged both similar jobs that involve collecting stuff on the surface - plant gathering and tree cutting - into one card 'Forestry and foraging' (name subject to change). But back to fortress building. There will be trait system in addition to resources. Main aspect of fortress design is of course balancing resources and defences but traits add some complexity to it. They determine the type of a card (dwarf/structure/place/event) its positioning (underground/surface) and other things. They determine relations with either player's or opponet's cards. Some cards may eg. target structures only, or may be played only if card with some trait is already in play. Some special effects of cards will add bonuses to cards with certain traits.
I hope that explains it, if not you're free to ask what is yet unclear - I'll happily answer.