You've just reminded me - a couple of months ago I locked my key in the boot. RACV came out and broke into the car for me so I could pop the boot with the glove box button. The alarm went off as soon as the dude opened my door and that was when we both learned that the boot release button in the glove box does not work if you break in. After pulling the emergency cable I was able to retrieve my key from the boot and hit the button to kill the alarm. After the car had been "unlocked" with the remote, the glove box boot release worked fine again.
I know this is not an answer to your problem, but it's a somewhat obscure bit of knowledge that might make everything make sense. Maybe. Or not.
When your car was broken into - how was the alarm disabled? By removing a bunch of relays or with the remote? I'm wondering if you now intentionally "break in" to your car, setting the alarm off, and then turn the alarm off with the remote, would it maybe "reset" the alarm/immobiliser, returning everything to normal status? I don't know, it just makes sense to me that this could be a thing. Can't hurt to try.