Sorry to hear Max, On my last car I was starting to get that after about 3 years and not driving it daily. Budds suggested that it could be due to not long enough trips in the car and not fully charging which ended up being the case. I ended up just leaving it on the trickle charger when I knew I wouldn't drive it for longer periods of time. I didnt have any issues with starting although I would get the warning and some times my clock would lose time. Never did they suggest it wouldn't be covered though if it was failing.
Seems to me you weren't treated right regardless if that's the real issue or not. Not locking your car properly, seriously WTF? I would have lost my mind on the guy who told me that.
Good Luck, hope you get it sorted