I've been playing around with the maximum size 100block multifarms, for now it's been mostly setting them up and just collecting their output in upgraded barrels. I did a test with some of the trees that are only obtainable through breeding, such as walnut, balsa, cherry, lime etc. The balsa and cherry grow and are collected just fine, which I was happy with, since this gave me an easy way of getting a large amount of different looking wood. The Balsa is particularly nice because it is a single trunk with sparse greenery, yet somehow manages to produce a solid amount of saplings fairly quickly...This may have to do with the fact that it can grow more balsa trees in a smaller area due to the aforementioned compact foliage. The multifarm won't grow a sapling if there is green foliage hanging in the air above the sapling after cutting down a tree, which was noticeable with trees that had heavy foliage. For this reason, having the balsa there has actually had the unintentional side effect of giving me more wood and saplings than I originally expected. It's also made our server's resident tree breeder excited due to the ease at which we can get all these saplings.
With trees that bear fruit, such as walnut / cherry trees, the multifarm doesnt seem intelligent enough to wait for the trees to mature, so you would only collect wood and saplings from those. The multifarm also doesn't seem to recognize the walnuts / cherries if you DO let them mature by either setting the system on a timer, or manually shutting it off. Our bee-keeper frowned at this realization, since this would have created a huge amount of seed oil for him to rub on his naked body or whatever bee enthusiasts do with the stuff. We did find a solution though, and that is to set up some wood golems in the area (preferably w/ quickness or strength), since when fully matured and chopped down, all the stuff falling from the leaves will make the golems go nuts (no pun intended).
Also, it's important to note that certain trees require more than 1 sapling in order to grow. Such as (again) the walnut tree, as it requires 4 saplings, I have yet to try the larger ones that require 9 saplings.. Multifarms throw down whatever sapling input is there with no consideration as to the breed, so if you put nothing but walnut saplings, you will of course have that 4 sapling requirement once the farm is done setting things up, and they will go on to grow and get chopped down as long as nothing changes. Good news for people trying to get more of a tree! (hence our resident tree-hugger's enthusiasm)
Geez I typed a lot...err sorry? Heh anyway I'll check in, I have more to add but its about time to eat something...