Some sort of underground foliage would be cool! Maybe some special herbs or berries that can grow in caves.
well how about caverns that have the sun shining in through a reeaaallly high up point and a special type of tree has evolved to live down there maybe like a giant shrub with berries on it when they flower (seasons thingy there) and when you clear that area out it can be where you grow your hops and other hardy plants for food, as of mining with them being dwarves how about they simply use some of the stone they harvest to make their beautifully crafted support pillars. also how about as a starting location they begin outside at the base of a mountain with a small brack nearby for initial wood n make a small base cam outside before making an entrance into the mountain and their main hall which you can expand as you mine further and then make additional chambers further along your shafts like an outpost or another town and make those shafts into main roads
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In Skyrim there is that underground area full of bio-luminescent plants that links up four of the ancient dwemer cities (canât remember itâs name for the life of me)
That is sort of what Iâm imagining but with more trees from your descriptions
Blackreach!
Theyâve stated that they would want the underground of the game to be the same as above ground, in that there is the same level of things to explore and discover, not just simply a mass block of dirt that you dig through.
DF has underground trees, so Stoneheart can have something simmilar. You could also start with a stash of wood for basic tools, then trade for more. Or dwarfs can just make everything out of stone, it will be a different play style after all.
I think I can hear them now: âWOOD laddie? We need no steenkinâ wood!â
or veins of petrified wood that you can mine like copper, haha I like how the dwarves are now Scottish, I can now hear them going : âay laddie I know oâ that wood stuff, them wee surface pansies use it, now go get me another piintâ (pint like that because they always say pie-nt) 
Petrified wood would be an option as well. I really like Reaperwright88âs idea, sort of like a tree in a cavern, with light shining on it from the overworld. Not really great but I guess this illustrates it pretty well: http://graphics.stanford.edu/courses/cs348b-competition/cs348b-09/finals/tree.png
the cavern idea fits with that the guys have said they want the underground to match the surface, I thought of the idea from dragon age with the dwarven section from there, so they could give a backdrop and have it so your a returning band of dwarves to re build a dwarven empire from these caverns and the linking tunnels with a huge main one for your city (obviously you can expand and change the shape of the caverns and tunnels)
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That sounds pretty awesome if you ask me! Instantly adds a lot of lore as well, which would explain why you would start of with a bunch of dwarves and all that 
Wood could also fall through holes in the ceilings of caverns b/c of topside chopping. The extra logs would just scatter around in a general area underneath the hole and could simply be collected. These could also have other things, like refined metals or tools, for example, but could also have strange mobs looting/sleeping/guarding these piles.
Just an added thought to the underground trees and such.
But what the dwarves should really do is punch stone with their bare hands and foreheads to retrieve the ore/stone. (Just kidding)
I really like this idea. I was thinking along these lines too. Dwarves would build out of stone instead of wood.
It does, I know the guys are reluctant to force lore on us(saying we can search it out if we want) but they have given a backdrop for the human settlers as s group whom have left the main kingdom for any reason you want, they can use a similar idea for the dwarves, you can pick that they start at an entrance to a mountain as your base camp and then you venture inside to either reclaim a lost territory or to start a whole new one ( or any other reason you can imagine that a dwarf might go separate from a kingdom) I like a base camp idea so that it gives a nice start rather than you just appearing with a group of dwarves in a cavern
I would reckon they use bare hands or stone tool, like our stone age to create tool from flint.
Fire would come from magma or firestone.
Yep, definitely! It would be a bit weird if dwarves would have to punch stone with their bare hands though. 
ahh well in the pre-pre-pre-pre alpha that the devs released to the youtubers your minions use axes on the trees, so the same could apply for picks to mine, Iâd like it if only your starting minions had the tools and with some stone and wood the carpenter can make axes and picks and hammers for your new minions when they âspawnâ yeah punching stone would look silly
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fist thing im doing when dwarfs come out is making it a rare mushroom calling it the magic mushroom and give my civilians an encumbered type effect
Minions? Makes you sound evil⊠Just back away slowlyâŠ
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Duuuuuudee, shrromms are psychedelick
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I am evil⊠well mostly, am a huuuuge overlord fan so minions be cool, think mushrooms are too cliché except the magic kind because duuuuuuude thats how the dwarves chill maan
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im sensing a theme here⊠
as for the OP, i wouldnt expect to see roots used (crafted) as part of the building process, but rather simply be integrated in the housing (think, carving out the landscape and retaining certain portions)⊠root systems running along roof lines, down walls, etc.