Well, I've discovered that there's an error on most of the boards. Fortunately, it's easy to work around.
I thought there would need to be a level shifter of some sort for the watchdog chip's WDI signal. So I added a MOSFET and pull-up to make this happen, but I used the footprint for a P channel MOSFET instead of an N, so it's wrong.
It turns out that you don't need a level shifter - the 3.3 volt high from the Pi is good enough on its own. So the fix is to replace the MOSFET with a 0Ω 0805 resistor going from the gate to the source pin (which is supposed to be the drain, but for the error). You also should leave out the 5 volt pull-up resistor that's on the watchdog chip's input. The 3.3 volt pull-up is all that's required (though these resistors are 100kΩ, so there's little harm in leaving them).
Version 4.0 has a similar error, but in this case the 0Ω resistor goes from source to drain.
In every case the idea is to just connect the WDI pin on the watchdog chip directly to GPIO4 on the Raspberry Pi header, with a 100 kΩ pull-up to 3.3 volts. This will be the design with 4.0.1 and beyond.