It is recommended that SYS_VIN_MV power on before SYS_VIN_HV.
AGX Orin Design Guide is being updated to correct the power sequencing information.
Did you use Software Shutdown command or power button to initiate shutdown? SW shutdown sequence would also be documented correctly in this upcoming design guide update.
SW shutdown is initiated through I2C command and MODULE_SHDN_N is not used during SW initiated shutdown and MODULE_SHDN_N will fall/droop along with the 1V8 rail.
The initial drop in voltage is due to the POR state of the pin and the internal pull down resistor. This internal pull down resistor forms a potential divider with the external pull up resistor used.