It's true it is the
BEM that keeps a record of which remote is set to two-stage unlock and which is set to one-staqe unlock. However it also depends on the remote accurately transmitting the button combination.
The OEM remote transmits the codes according to the buttons pressed (and the
BEM works out how to interpret the message) and, if multiple buttons are pressed, the remote says so. The clone remote must be only signalling that one button is pressed, even if more than one is pressed. The software must stop checking the other buttons after it confirms the first one is pressed.
They must have missed the subtle difference when doing their reverse-engineering.