1. I'm not sure on the aboveground trees(I just cut those down), but I've had a small drainage channel in my current fort that has towercap saplings for over 6 years now, and only one out of about 20 of them grew to be big enough to harvest. There are also a lot of shrubs.
2. I do not forbid anything outside(Waste of time with the seemingly random growth), but an eventual towercap farm will have a single tile wide paved road, with 2 tile wide trees/shrubarea in between roads, like exploratory mining, but with wood. I plan to have the growing areas all set as restricted and the roads as high, so dwarves will only walk on the plants if they need what is in that tile.
3. trees can grow 1z below their normal starting level when the ground is channelled, but I only know this with another layer of soil below the first(No idea on rock), and it was a small, short-lived fort, so I don't know a lot on this part.
4. As soon as the message of finding underground water(River/pool) has been shown, any water used to make muddy ground(Underground) will be able to grow towercaps, this includes the channels made for getting fresh, aboveground brook water into a cistern, I have found myself ordering blocking towercaps to be cut down several times. These will still display the ~ from water, and you need to use k or every now and then designate all your channels for having trees cut down.
In short, any underground mud will do after you got the message.