The easiest way to prevent Universal Module from raising the garage door is to wire a magnetic window switch in series with the Universal Module which is wired to short across the lifters wired wall switch switch (more on this, I saw Brian's comment that your wired switch is a multi control). Position the magnet for the window switch so they line up only when the door is open. Thus when the door is closed the window switch is open and the Universal Module can not short across the wall switch.
Our garage door opener also has multi control function, however it works by varying current levels back to the opener. So a dead short is the opener activation signal. Higher resistance shorts result in garage light control and "Vacation" control. This does not mean the Lift Master works the same way, but since it is a fail safe way of operating the wired switch circuit in the event an owner likes his old door bell style button, or wants to use one of the "universal" electronic combination keypads, I bet it does.