1) There is a mistake in the schematic: it should be S1, S2, S3 all connect to the 0 ohm resistor, and COMT connected directly to ground. The 0 ohm resistor is reserved for future use and is to be replaced by a current sensing resistor, such as 0.2 ohm (same as on OpenSprinkler 3.0). It will be used to sense current (but this is only useful when the controller is in non-latching mode, since in latching mode the current is instantaneous and there is no point trying to measure it).
So if you don’t need current sensing, just connect all to ground. The schematic is showing a 0 ohm resistor anyways, so it’s equivalent to be connected to GND.
2) Same as above, it should be S1, S2, S3 connected to analog pin.
3) As you must have noticed, COMT and S1, S2, S3 use exactly the same design, it’s basically a half H-bridge each. This allows each port to be connected to either GND or boosted voltage. You can read the technical details here: