My 2 cents the AP measurement of latency via non-AP playback chain (i.e. via some third-party audio interface, using windows audio drivers) is not designed to work correctly and yields irrelevant data. Just for the reason you ask about - the hardware (which measures the latency for the SPDIF generator-ADC case) would have to know somehow (without latency) when software outputs data to the driver buffer. Plus still latency of the whole driver chain would be included.
It looks like it just measures loopback latency out/in in software, where latency of the input capture is included - AP has no practical reason to minimize/keep constant the latency of the data transfer from their HW to the software, plus IIUC it does not use USB audio for data acquisition from their device, but some custom protocol.
IMO that shows that Amir would have to use some other method which is getting quite complicated - IIUC he has some set of measurements pre-configured in his AP software and the whole test runs more or less automatically.