Temperature and moisture don't appear to update. I checked some cliff plots with extreme differences between the z levels of various blocks, and the temperature doesn't change. Likewise, irrigation - if it's working as intended - ignores z levels at the moment. You should even be able to create a floating farm this way. On mountainous maps you can use this to your advantage by excavating farm areas into cliff sides.
You can also take a triple optimal plot and build a farm tower. Even bushes don't seem to suffer much from extreme overcrowding, and with high enough skill levels you'll get a minimum yield of 6 per plant anyway, even if base yield is only 1.