I am not using the 1F controller, so am not sure about any soft/hard limits that might interfere with this sub waste board cutting. Perhaps it could be done in a slow, careful, and controlled manner using the game pad to execute the cuts?
I found this reference to someone who cut dog holes through the spoil board, and the router mount was in the middle position. So for your question, it seems that lowering the mount to the lowest/bottom position, should get you through the table, especially if you invest in a longer cut length endmill (but maybe you won’t have too - will depend on your table thickness).