THanks a lot, nice detailed photos and video.
The problem is your Pi takes forever to shutdown. The board waits around 50seconds for the shutdown to complete (BOOTOK to be turned OFF by Pi). If that does not happen in that much time, ATXRaspi does not know what is going on, and will keep power ON (for safety reasons, to avoid cutting power off when in fact something happens for a good reason and BOOTOK does not go LOW).
In all my testing and experience I never saw a Pi shut down so slowly, so that 50s delay was always a lot more than expected. Your Pi takes almost 70 seconds to shut down!
We can change that final delay in firmware to more. But how much is really reasonable without causing other problems?
If you return the board to me I can increase the final delay, or maybe you can try to improve the Pi to shut down faster?