the tree root idea would probably have to wait until toady does trees that span more then one z level, something i really like the idea of, though cutting them down will involve a whole lot of problems in regards to dwarves getting squished by falling trees as they swarm around collecting wood. im sure toady has somethign like this in mind, he has treetop elf towns in his list of things he would like to do eventually.
and, in regards to coal fires, they can go for centuries. and people dont not notice they are going, they tend to just leave them, as most are started in mining accidents, and its incredibly hard and expensive to put them out. there is one in the novel "lady chatterlies lover" in the area the story takes place, which gives the little english town a whole unpleasant hellish feel to it what with the constant smoke and smell and ash when the wind is the wrong way.
here in australia we have a natural coal fire, at a place called burning mountain. there are a few naturally occuring ones around the world, started by surface fires or ligtening strikes. from wikipedia - 'According to Smithsonian Magazine, "Scientists estimate that Australia's Burning Mountain, the oldest known coal fire, has burned for 6,000 years."' thats a very long time.
so underground coal fires could be a site feature you could embark on. that would be interesting and challenging, and could potentially involve unique creatures like fire imps.