@vcapra1, The MSFS ON/OFF commands, like the ones for the lights, use two separate commands, one for the ON switch position and one for the OFF position of a toggle switch. If you use these commands the switch cannot be changed in the cockpit with the mouse because it will held in the ON or OFF position by the commands being continuously sent from the Honeycomb switch... But, the SET command uses only one command which is bound to the ON position of the toggle switch, or to a button. When the toggle switch is flipped ON, or button is held down, the ON command is sent to the sim, and when it is released the function is then toggled back OFF, and it is then free to be controlled by the mouse. It sounds like that might be how yours is already set up, since you can control it with the mouse when the ALPHA switch is OFF.
The autopilot buttons on the BRAVO are not toggle switches, they are buttons, and are programed by the BRAVO software driver to send the required commands to turn the function ON or OFF. And, since they are not held down and the command is only sent once it doesn't interfere with the mouse control.