I saw no roots, but I did see one cavern collapse message after chopping a large fungiwood down, but only the one time.
After six years total, that is, after 3 years of growth after maturing, the numbers I posted above for logs per mushroom-tree are identical. It may be that much older mushroom-trees produce more logs, but not after 3+ years of mature growth.
Also, the tallest tree height reached over the 3 years of mature growth was six Z-Levels. The base of the three was at 122, the max height branch/tip was at 127. Both bloodthorn and fungiwood reached this height. There was 10 Z's to grow in, so they weren't restricted by the "cave" height.
Finally, goblin caps and black caps did not grow to the same size as "natural" ones do, in the worldgen caverns. In this artificial "cave" they only made short stubby spikes 2Z tall, rather than the full sized mushroom-trees you normally see. It's possible this is due to insufficient x-y area for crown growth. Tunnel tubes, similarly, were stunted in that they didn't bifurcate as much, nor grow as tall as normal.