This is an interesting thing, how that came to be. We didn't have any reason to make trees big; the average tree height comes from numbers specified by "official" figures for given species. If you turn on the HUD (tab key) showing the elevation, and subtract top and bottom, you get the right numbers. So what's the problem?
Well, after some digging around, apparently the textures of mature trees we used are not of the typical maximum tree height given for most of the species. The reason seems to be that the textures are usually made based on standalone tree samples, because of better accessibility and visibility, but lone trees usually grow shorter (and wider) than ones in groves, where they have to compete for sunlight.
Obviously when the lone tree images are scaled to the height of the grove trees, we get enormous looking ones ...
The easiest way would be to scale them down uniformly, even though not all species are mismatched equally.