Hi Jason.
After a quick test just in case on chapter 1 (using "r", "t" and "s 10" commands from the console (respectively for resources, all techs and speed of 10) and shift F4 to switch player) here are my conclusions.
The guard tower will attack if the enemy is close enough, in the same square or not (didn't test diagonals but it should work too).
A human player can ignore the towers by giving an imperative order and target important buildings or just pass through. If the map have squares with a big size the range of the tower might not be enough. An AI could ignore towers too but is not programmed to do it at the moment.
Building a wall or a gate might prevent this.
Hope it helps.