If I understand correctly how the game works, that's not possible in Factorio. Factorio allows up to 2 players to ride in the same vehicle (driver and passenger). There's a switch where you can toggle which player is in control of the guns: it's either the driver or the passenger. This can also be toggled by mods (which Autodrive already does if only one player is in the vehicle who does the driving; it creates a dummy character if enemies are detected who operates the gun in that case).
Autodrive checks each vehicle on each tick and automatically fires the chosen weapon if the dummy passenger is in control of the gun. I certainly could assign a target to the dummy passenger, then set driver_is_gunner to true and choose the second gun. But that would automatically take gun control away from the passenger, so the vehicle would still use one gun only.
There might be a workaround, but it's such a dirty hack that I wouldn't dare to try it (also, it probably would lead to an UPS load that would be insane): Remove all but the first gun from the vehicle, create a second vehicle that gets the secondary weapon (perhaps even a third vehicle for the tertiary weapon --> tanks!) on top of the first, place another dummy in it and let it be the gunner. There now would be two (or three) vehicles that could shoot independently. But this would also mean I'd have to keep track of the second vehicle all the time, change the code for reloading so that the other vehicles will reload from the trunk of the first, and keep track of the damage all vehicles take so that the vehicle doesn't magically get double or triple health. I guess it could be done, but it clearly is a straight road to insanity which I'm not willing to take. Moreover, things would break everywhere, and the toll on UPS would be way to high. (Also, I can already see the requests coming in for extending this to the fourth or fifth guns other mods may have given to their vehicles -- where would it end?)