1. Why do the dynamics of unsaturated water look so much smoother in this model if compared to the model for unsaturated water only?
In the unsaturated zone-only model, water that percolates out of the unsaturated zone is lost from the system. In the newer model, water that percolates out of the unsaturated zone enters the saturated zone. As a result, when precipitation falls and the site dries out, the unsaturated zone will recover water from the saturated zone, which will stabilize its levels. This wasn't possible in the older model because that water had left the system.
As evidence of this, notice that when precipitation falls, around day 200, percolation goes deeply negative and water moves from the saturated to the unsaturated zone. A miniature version of similar dynamics occurs again around day 600.
2. Can you make all the ground saturated and the unsaturated layer
disappear from the system? What parameters need to be changed?
What is their ecological meaning?
Is it just me or is this question, A) weird, and B) trivial?
That said, you have to check the "non-negative" boxes for both stocks, to make this happen, but that's physically legitimate -- you can't have a negative amount of ground water.
Cranking transpiration up by an order of magnitude causes both stocks to go to zero within a year:
The ecological meaning of this is that plants are pulling more water out of the unsaturated layer, from whence it evaporates through their leaves, and the unsaturated water, in turn, sucks water from the saturated water, which then also ends up moving through the plants.