I've had this happen twice in the past few days, never happened before; when I unlock the wagon via the tailgate (unlocks all doors), and then open the tailgate, the alarm (horn) has gone off. Need to go to the driver's door and flick the key in the lock to turn it off.
We tried various scenarios today to replicate it, but couldn't; locking car via door then unlocking via tailgate, locking via tailgate then unlocking via tailgate, etc.

We lock/unlock via the tailgate quite a bit, as we only have one remote and that one's playing up, and we have a 2yr old that we need to get into the rear passenger side first.

Any thoughts? Did a search and didn't turn up anything.

I have an issue where my alarm wont set when the boot isn't shut properly, I would suggest checking the wiring with a multimeter and ensure that it is working correctly. My bet would be a loose wire or connector.

Maybe the switch is shorting and setting the alarm off?

Head down to your local Jaycar and get a push button switch. Wire that in instead and see if it makes a difference.

Alternatively just disconnect the tailgate sensor/switch and leave it be?

An update; have paid more attention, and what's happening is that half the time on turning the key the central locking isn't activated - ie., the tailgate physically unlocks, but nothing else does and the alarm thinks it's still locked, hence alarm on opening. It's becoming more common, we now kee an ear out to make sure the central locking activates.
Will see if I get some time to pull apart the tailgate lock and have a look.

An update; have paid more attention, and what's happening is that half the time on turning the key the central locking isn't activated - ie., the tailgate physically unlocks, but nothing else does and the alarm thinks it's still locked, hence alarm on opening. It's becoming more common, we now kee an ear out to make sure the central locking activates.
Will see if I get some time to pull apart the tailgate lock and have a look.

Take pictures when you do because mine does the same - occasionally. lol