Right now, trees seem fairly gigantic in comparison to most buildings and people. Each seems about 3-6 z levels high, while most human buildings are 1-3. The trunks are 2x2 but people are just 1 tile, making each tree like some kind of great big baobab or sequoia.
Your perception of scale is all kinds of messed up. Do you live in a city or something? There's very few trees that don't get to be twice the height of a single story house in just a few years, and double the width of a human can be as little as a few decades. Since these are presumably natural-growing trees (rather than planted by landscapers or loggers) many of them are likely hundreds of years old. The current size/shape seems to be modeled on oaks, and is appropriate to a lot of deciduous trees. It would be cool to see some trees that really do redwoods justice, but they would be a lot taller than anything in the game currently, besides geological features such as mountains. I believe they're not in because of the hardware issues implicit in calculating all those extra Z-levels, although a fort or elven encampment in a redwood forest would be incredibly awesome.
But the trees even surpass many human forts, which is obviously not so good for the fort. And if 2x2 is supposed to be the size of an average bedroom, then that's an enormous tree. An adult human can wrap his/her arms around or almost around most trees.
You are confusing sleeping quarters in a wealthy area of modern society with those of medieval peasants. And you are confusing trees that have been around for a relatively short period (read: almost all trees you're likely to have seen, unless you live in the right place) with trees that have stood for millennia (most of which near where most people live have long (and I really do mean long here) since been felled.
There are very few tree species with natural lifespans that long. And I'm not confusing wealthy modern bedrooms with medeival ones. A tree the girth of a room which can hold a bed, a chest, and a cabinet is a very fat tree indeed. Hell, even a tree with the girth of just a bed is huge. The trees I can think of which approach that size are redwoods, sugar-cone pines, sequoias, figs, baobabs, and certain tropical hardwoods. Oaks, spruces, elms, firs, willows, maples, larches, yews, fruit trees, and pretty anything else you'd find outside a rainforest doesn't approach that girth. I live in a suburb and often visit mountains and national forests, and I've seen giant sequoias up close.
As for Z-levels, I don't think 1 z-level equals 1 foot, more like 10. 20 z levels should be sufficient to represent a redwood or giant sequoia. Using that math, that makes mountains around 2,000-4,000 feet high, a realistic mountain size.